Full wwPDB EM Map/Model Validation Report iO

Aug 22, 2020 � 04:38 PM BST

PDB ID : 6CGREMDB ID : EMD-7472

Title : CryoEM structure of herpes simplex virus 1 capsid with associated tegumentprotein complexes.

Authors : Dai, X.H.; Zhou, Z.H.Deposited on : 2018-02-20Resolution : 4.20 Å(reported)

This is a Full wwPDB EM Map/Model Validation Report for a publicly released PDB entry.

We welcome your comments at validation@mail.wwpdb.orgA user guide is available at

https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

EMDB validation analysis : 0.0.0.dev33MolProbity : 4.02b-467

Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.13

Page 2 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY

The reported resolution of this entry is 4.20 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricWhole archive(#Entries)

EM structures(#Entries)

Ramachandran outliers 154571 4023Sidechain outliers 154315 3826

The table below summarises the geometric issues observed across the polymeric chains and their�t to the map. The red, orange, yellow and green segments on the bar indicate the fraction ofresidues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. Agrey segment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor �t to the EMmap (all atom inclusion < 40%). The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 4 1374

1 A 1374

1 B 1374

1 C 1374

1 D 1374

1 E 1374

1 F 1374

1 M 1374

1 N 1374Continued on next page...

Page 3 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

Continued from previous page...

Mol Chain Length Quality of chain

1 O 1374

1 S 1374

1 T 1374

1 U 1374

1 V 1374

1 W 1374

1 X 1374

2 0 112

2 1 112

2 2 112

2 3 112

2 G 112

2 H 112

2 I 112

2 J 112

2 K 112

2 L 112

2 P 112

2 Q 112

2 R 112

2 Y 112

2 Z 112

3 5 465

3 8 465

3 b 465Continued on next page...

Page 4 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

Continued from previous page...

Mol Chain Length Quality of chain

3 e 465

3 h 465

4 6 318

4 7 318

4 9 318

4 a 318

4 c 318

4 d 318

4 f 318

4 g 318

4 i 318

4 j 318

5 k 703

6 l 580

6 m 580

7 n 3139

7 o 3139

Page 5 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

2 Entry composition iO

There are 7 unique types of molecules in this entry. The entry contains 219702 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the AltConf column contains the number of residues with at least one atomin alternate conformation and the Trace column contains the number of residues modelled with atmost 2 atoms.

� Molecule 1 is a protein called Major capsid protein.

Mol Chain Residues Atoms AltConf Trace

1 A 1362Total C N O S10409 6575 1871 1909 54

0 0

1 B 1364Total C N O S10423 6585 1873 1911 54

0 0

1 C 1364Total C N O S10423 6585 1873 1911 54

0 0

1 D 1362Total C N O S10409 6575 1871 1909 54

0 0

1 E 1366Total C N O S10442 6595 1878 1915 54

0 0

1 F 1362Total C N O S10409 6575 1871 1909 54

0 0

1 M 1362Total C N O S10409 6575 1871 1909 54

0 0

1 N 1366Total C N O S10442 6595 1878 1915 54

0 0

1 O 1364Total C N O S10423 6585 1873 1911 54

0 0

1 S 1357Total C N O S10365 6547 1864 1900 54

0 0

1 T 1357Total C N O S10379 6553 1868 1904 54

0 0

1 U 1364Total C N O S10423 6585 1873 1911 54

0 0

1 V 1362Total C N O S10409 6575 1871 1909 54

0 0

1 W 1364Total C N O S10423 6585 1873 1911 54

0 0

1 X 1348Total C N O S10314 6516 1857 1888 53

0 0

1 4 1259Total C N O S9648 6103 1726 1769 50

0 0

� Molecule 2 is a protein called Small capsomere-interacting protein.

Page 6 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

Mol Chain Residues Atoms AltConf Trace

2 G 101Total C N O S774 488 146 137 3

0 0

2 H 101Total C N O S774 488 146 137 3

0 0

2 I 101Total C N O S774 488 146 137 3

0 0

2 J 101Total C N O S774 488 146 137 3

0 0

2 K 101Total C N O S774 488 146 137 3

0 0

2 L 101Total C N O S774 488 146 137 3

0 0

2 P 101Total C N O S774 488 146 137 3

0 0

2 Q 101Total C N O S774 488 146 137 3

0 0

2 R 101Total C N O S774 488 146 137 3

0 0

2 Y 101Total C N O S774 488 146 137 3

0 0

2 Z 101Total C N O S774 488 146 137 3

0 0

2 0 101Total C N O S774 488 146 137 3

0 0

2 1 101Total C N O S774 488 146 137 3

0 0

2 2 101Total C N O S774 488 146 137 3

0 0

2 3 101Total C N O S774 488 146 137 3

0 0

� Molecule 3 is a protein called Triplex capsid protein 1.

Mol Chain Residues Atoms AltConf Trace

3 5 353Total C N O S2724 1708 518 481 17

0 0

3 8 363Total C N O S2786 1741 531 496 18

0 0

3 b 363Total C N O S2786 1741 531 496 18

0 0

3 e 352Total C N O S2720 1706 517 480 17

0 0

3 h 353Total C N O S2724 1708 518 481 17

0 0

Page 7 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

� Molecule 4 is a protein called Triplex capsid protein 2.

Mol Chain Residues Atoms AltConf Trace

4 6 276Total C N O S2116 1354 375 380 7

0 0

4 7 308Total C N O S2341 1487 415 430 9

0 0

4 9 274Total C N O S2091 1338 370 376 7

0 0

4 a 308Total C N O S2341 1487 415 430 9

0 0

4 c 274Total C N O S2091 1338 370 376 7

0 0

4 d 308Total C N O S2341 1487 415 430 9

0 0

4 f 272Total C N O S2089 1337 371 374 7

0 0

4 g 308Total C N O S2341 1487 415 430 9

0 0

4 i 276Total C N O S2116 1354 375 380 7

0 0

4 j 308Total C N O S2341 1487 415 430 9

0 0

� Molecule 5 is a protein called Capsid vertex component 1.

Mol Chain Residues Atoms AltConf Trace

5 k 550Total C N O S4206 2674 764 747 21

0 0

� Molecule 6 is a protein called Capsid vertex component 2.

Mol Chain Residues Atoms AltConf Trace

6 l 94Total C N O S766 486 138 138 4

0 0

6 m 80Total C N O S654 413 124 115 2

0 0

� Molecule 7 is a protein called Large tegument protein deneddylase.

Mol Chain Residues Atoms AltConf Trace

7 n 47Total C N O S384 237 84 61 2

0 0

7 o 47Total C N O S384 237 84 61 2

0 0

Page 8 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

3 Residue-property plots iO

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andatom inclusion in map density. Residues are color-coded according to the number of geometricquality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2and red = 3 or more. A red diamond above a residue indicates a poor �t to the EM map forthis residue (all atom inclusion < 40%). Stretches of 2 or more consecutive residues without anyoutlier are shown as a green connector. Residues present in the sample, but not in the model, areshown in grey.

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• Molecule 1: Major capsid protein

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Page 9 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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• Molecule 1: Major capsid protein

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• Molecule 1: Major capsid protein

Page 10 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

Chain D:

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• Molecule 1: Major capsid protein

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Page 11 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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• Molecule 1: Major capsid protein

Chain F:

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• Molecule 1: Major capsid protein

Chain M:

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Page 12 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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• Molecule 1: Major capsid protein

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• Molecule 1: Major capsid protein

Chain O:

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Page 13 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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• Molecule 1: Major capsid protein

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Page 14 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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• Molecule 1: Major capsid protein

Chain T:

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Page 15 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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Page 16 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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• Molecule 1: Major capsid protein

Chain X:

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Page 17 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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Chain 4:

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Page 18 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

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• Molecule 2: Small capsomere-interacting protein

Chain G:

Page 19 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

MET

ALA

V3

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Q5

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• Molecule 2: Small capsomere-interacting protein

Chain H:

MET

ALA

V3

F6

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R8

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D15

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PRO

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GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain I:

MET

ALA

V3

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Q5

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D15

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PRO

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PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain J:

MET

ALA

V3

�P4

Q5

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T13

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D15

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A19

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R51

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PRO

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PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain K:

MET

ALA

V3

P4

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R8

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D15

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R18

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G81

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Page 20 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

D82

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GLU

PRO

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PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain L:

MET

ALA

V3

�P4

Q5

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H7

�R8

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S10

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V12

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GLU

PRO

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PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain P:

MET

ALA

V3

�P4

Q5

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R8

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D15

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A69

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A80

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GLU

PRO

SER

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PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain Q:

MET

ALA

V3

�P4

Q5

�F6

�H7

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V12

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D15

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R18

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A58

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L66

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ARG

GLU

PRO

SER

THR

PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain R:

MET

ALA

V3

P4

Q5

�F6

�H7

R8

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D15

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R18

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G21

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ARG

GLU

PRO

SER

THR

PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Page 21 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

Chain Y:

MET

ALA

V3

�P4

�Q5

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T11

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T13

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H42

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A49

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A59

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G65

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A67

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M78

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A80

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GLU

PRO

SER

THR

PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain Z:

MET

ALA

V3

�P4

�Q5

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S10

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T14

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A86

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A91

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S99

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GLU

PRO

SER

THR

PRO

GLY

THR

PRO

• Molecule 2: Small capsomere-interacting protein

Chain 0:

MET

ALA

V3

P4

�Q5

�F6

�H7

�R8

�P9

S10

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D15

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R18

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L27

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ARG

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PRO

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• Molecule 2: Small capsomere-interacting protein

Chain 1:

MET

ALA

V3

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Q5

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N71

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PRO

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• Molecule 2: Small capsomere-interacting protein

Chain 2:

MET

ALA

V3

F6

�H7

�R8

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T11

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D15

�S16

�V17

R18

�A19

�L20

�G21

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A28

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Page 22 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

N70

�N71

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Q76

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M78

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G81

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V103

ARG

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• Molecule 2: Small capsomere-interacting protein

Chain 3:

MET

ALA

V3

P4

Q5

�F6

�H7

�R8

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T13

�T14

�D15

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N70

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• Molecule 3: Triplex capsid protein 1

Chain 5:

MET

LYS

THR

ASN

PRO

LEU

PRO

ALA

THR

PRO

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VAL

TRP

GLY

GLY

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THR

VAL

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ASP

THR

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LYS

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• Molecule 3: Triplex capsid protein 1

Chain 8:

MET

LYS

THR

ASN

PRO

LEU

PRO

ALA

THR

PRO

SER

VAL

TRP

GLY

GLY

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THR

VAL

GLU

LEU

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ARG

ASP

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GLY

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GLY

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LEU

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ARG

VAL

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GLY

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GLY

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GLY

ALA

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ASN

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ASP

THR

GLU

GLN

ALA

LEU

ASP

LYS

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GLY

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GLY

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ALA

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G103

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Page 23 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

A379�

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• Molecule 3: Triplex capsid protein 1

Chain b:

MET

LYS

THR

ASN

PRO

LEU

PRO

ALA

THR

PRO

SER

VAL

TRP

GLY

GLY

SER

THR

VAL

GLU

LEU

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ASP

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ALA

GLY

GLN

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ARG

VAL

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ASP

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ALA

ALA

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ASP

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• Molecule 3: Triplex capsid protein 1

Chain e:

MET

LYS

THR

ASN

PRO

LEU

PRO

ALA

THR

PRO

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VAL

TRP

GLY

GLY

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THR

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• Molecule 3: Triplex capsid protein 1

Chain h:

MET

LYS

THR

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LEU

PRO

ALA

THR

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VAL

TRP

GLY

GLY

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THR

VAL

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ARG

ASP

THR

ALA

GLY

GLN

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ASP

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GLY

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Page 24 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

G157�

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ARG

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• Molecule 4: Triplex capsid protein 2

Chain 6:

MET

LEU

ALA

ASP

GLY

F6

D9

�I10

A11

�I12

P13

�S14

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I16

�S17

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A22

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GLY

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S57

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D59

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L79

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• Molecule 4: Triplex capsid protein 2

Chain 7:

M1

�L2

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• Molecule 4: Triplex capsid protein 2

Chain 9:

MET

LEU

ALA

ASP

GLY

F6

R18

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ASP

VAL

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GLN

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Page 25 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

V198�

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• Molecule 4: Triplex capsid protein 2

Chain a:

M1

A11

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R26

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• Molecule 4: Triplex capsid protein 2

Chain c:

MET

LEU

ALA

ASP

GLY

F6

E7

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I16

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R18

P19

D20

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A22

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GLY

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G196

P197�

V198

N199�

E215�

F228�

A229

L230�

S231�

A232

Q233�

D234�

L241�

V246

THR

ARG

GLU

ALA

ALA

GLN

LEU

ILE

HIS

PRO

GLU

ALA

PRO

ALA

LEU

MET

GLN

ASP

GLY

GLU

R267�

R268�

E273�

G283�

G286�

D287�

R296�

R307�

D310�

R316�

Y317

P318�

• Molecule 4: Triplex capsid protein 2

Chain d:

M1

�

D4

�

D20

�

R26

�C27

E28

�

I37

E49

�

G55

�

L63

R69

�

R77

G111�

E122�

G123

Q124�

A125�

T126�

L130�

R149�

R158�

G159�

D162�

L163

N164

PRO

SER

PRO

ARG

ASN

PRO

GLY

GLY

LEU

PRO

D175�

L188�

L189

A190�

D191�

V192

Q193�

M209�

V210

Y211�

L221�

A239�

L240

L241

Q242

M243�

R248�

E249�

I254�

H255�

A260�

E273�

A292�

P318�

• Molecule 4: Triplex capsid protein 2

Chain f:

MET

LEU

ALA

ASP

GLY

F6

E7

�T8

D9

�

G15

�I16

S17

�R18

�P19

D20

�

R26

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R39

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D45

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V52

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GLY

GLY

VAL

S57

T76

L92

�

A95

�G96

�

F121�

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GLY

GLN

ALA

THR

D127

R161�

D162�

L163

ASN

PRO

SER

PRO

ARG

ASN

PRO

GLY

GLY

LEU

Page 26 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

PRO

ASP

L176

S184�

L188�

L189�

A190

ASP

VAL

GLN

GLN

L195�

G196�

N199�

L202

E215�

R226�

L230�

S231

A232�

Q233�

D234�

N238�

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ALA

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LEU

ILE

HIS

PRO

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ALA

PRO

ALA

LEU

MET

GLN

ASP

GLY

GLU

R267�

R268�

E273�

A274

L275�

D287�

R296�

D301�

R307�

D310�

M311�

P318

• Molecule 4: Triplex capsid protein 2

Chain g:

M1

�L2

�A3

�

G15

�

I37

R38

R39

�

A44

�

E49

�S50

�

S53

�G54

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A125�

T126

D127�

D131�

D134�

L135�

R138�

R149�

D162�

L163

N164

PRO

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PRO

ARG

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PRO

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GLY

LEU

PRO

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L179�

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D191

V192�

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N199�

L207�

E215�

G216�

I219�

I220

L221�

R226�

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L241

Q242

M243�

Q244

S245�

R248�

E249�

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H255�

P256

E257�

A258

P259�

A260�

L261�

M262�

Q263�

D264

G265�

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R267�

E273�

A277�

Q284�

D287�

A292�

D301�

G302�

A303�

R307�

D310�

P318�

• Molecule 4: Triplex capsid protein 2

Chain i:

MET

LEU

ALA

ASP

GLY

F6

E7

�

R18

�P19

D20

�

R26

�C27

E28

�

Q40

�

D45

�

E49

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V52

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GLY

GLY

VAL

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P58

D59

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G62

�

R77

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L92

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H94

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PRO

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PRO

ARG

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PRO

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L173�

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VAL

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GLN

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PRO

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MET

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ASP

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GLU

R267�

R268�

A277�

D287�

D301�

G302�

R307�

D310�

R316�

Y317

P318

• Molecule 4: Triplex capsid protein 2

Chain j:

M1

�L2

�

E7

�T8

D9

�

I37

R38

�R39

�

D45

�V46

A47

�H48

E49

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G55

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D127�

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N164�

PRO

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PRO

ARG

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PRO

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GLY

LEU

PRO

D175�

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L207�

N208

M209�

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L241

Q242

M243�

Q252�

L253�

I254

H255�

P256

E257�

A260�

D301�

G302�

R307�

R316�

Y317

P318�

• Molecule 5: Capsid vertex component 1

Page 27 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

Chain k:M1

�

D12

�L13

�G14

H15

�GLY

PRO

GLY

ARG

P20

�S21

�

H25

�

E31

�C32

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G37

�

M44

�R45

�GLY

ARG

PRO

GLY

LEU

GLY

THR

ALA

A54

�N55

�F56

Q57

�V58

E59

�

R63

�

A66

�

D69

�C70

�

A76

�

Y80

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D84

�A85

�V86

G87

�E88

L89

�

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�L100

L101�

P102�

R103

A104

S105�

S106

A107�

L110�

V117�

C118

D119�

A120�

Q121�

G122�

D125�

P126

Y127�

A128

V129�

G137�

S138�

G139

A140�

R144�

V145

I146�

E152�

N157�

T158

R159�

D163�

R166�

R169�

V170

C171�

R172�

C175�

R176�

Y177�

V178�

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A183�

A184�

A185�

A189�

K190�

E191�

A192

A193�

L196�

S197

M198�

G199�

L200�

GLY

GLU

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ALA

SER

PRO

ARG

PRO

GLN

PRO

LEU

ALA

ARG

PRO

HIS

ALA

GLY

ALA

PRO

ALA

ASP

PRO

PRO

ILE

VAL

GLY

ALA

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ASP

P230

E235�

E236�

Q237

L238�

P241�

G242�

G243�

D244�

T245�

T246�

A247�

A248�

Q249�

D250�

V251�

S252�

I253�

A254�

Q255�

E256�

N257�

E258�

E259�

I260�

L261�

A262�

L263�

V264�

Q265�

R266�

ALA

VAL

GLN

ASP

VAL

THR

ARG

ARG

HIS

PRO

VAL

ARG

ALA

ARG

THR

GLY

ARG

ALA

ALA

CYS

GLY

VAL

ALA

SER

GLY

LEU

ARG

GLN

GLY

ALA

LEU

VAL

HIS

GLN

ALA

VAL

SER

GLY

GLY

ALA

MET

GLY

ALA

ALA

ASP

ALA

ASP

ALA

VAL

LEU

ALA

GLY

LEU

GLU

PRO

PRO

GLY

GLY

GLY

ARG

PHE

VAL

ALA

PRO

ALA

PRO

HIS

GLY

PRO

GLY

GLY

GLU

ASP

ILE

LEU

ASN

ASP

VAL

LEU

THR

LEU

THR

PRO

GLY

THR

ALA

LYS

PRO

R355�

S356�

L357�

V358

E359�

W360

L361�

D362�

R363�

G364

W365�

E366�

A367

L368�

G371�

D372�

R373�

P374

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R380�

R381�

S382

I383�

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G392�

Q395�

R396�

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G410�

R411�

R412

A413�

R414�

P415�

P416

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L418�

A421�

L422�

A423�

L426�

T427�

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A431�

A432�

E433�

R434�

V435�

V436

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P438

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Q440�

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G445�

Q446�

A447

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L451�

R452�

F453�

P454

A455�

L456�

E457�

L460�

R461�

H462�

P463

R464�

L467�

P468�

P469

F470�

D471�

I472

A473�

A474�

F478�

R481�

A489�

Q492�

A496�

A497

L498�

Q499�

G500�

R503�

D511�

Q516�

G521�

R525�

L531�

E532

N533�

L534�

M535

R536�

E539�

G540�

D544�

H548�

G561�

R562�

GLY

GLY

ARG

GLY

ARG

ARG

V569�

D575�

D582�

S583�

D584�

G585�

D590�

D597�

N603�

R604�

M610�

D611�

GLY

ASP

VAL

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LYS

ARG

E618�

Q619�

S620�

K621

C622�

R623�

E626�

A627�

VAL

PRO

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THR

ALA

P633�

R634�

E638�

L641�

G652�

R655�

R656�

G659�

F667�

A675�

Y676�

L677�

S678�

L679�

S680�

D681�

R685�

A686

A687�

F691�

C692

R693�

K694�

V695

S696�

SER

GLY

ASN

GLY

ARG

SER

ARG

• Molecule 6: Capsid vertex component 2

Chain l:

M1

�D2

�

D8

�A9

L10

�D11

�V12

W13

�E14

�H15

�R16

�R17

�

V20

�A21

�D22

�S23

R24

�

D34

�F35

�

N42

�L43

P44

�R45

�E46

�T47

�A48

�

Q51

�

V54

�L55

�Q56

A57

�Q58

�R59

�T60

�

A63

�A64

�A65

�L66

�E67

N68

�A69

�A70

�M71

�Q72

�A73

�A74

�E75

�L76

�P77

�V78

�D79

�I80

�E81

�

R82�

R83�

L84�

R85�

P86�

I87�

E88�

R89�

N90�

V91�

H92�

E93�

I94�

ALA

GLY

ALA

LEU

GLU

ALA

LEU

GLU

THR

ALA

ALA

ALA

ALA

ALA

GLU

GLU

ALA

ASP

ALA

ALA

ARG

GLY

ASP

GLU

PRO

ALA

GLY

GLY

GLY

ASP

GLY

GLY

ALA

PRO

PRO

GLY

LEU

ALA

VAL

ALA

GLU

MET

GLU

VAL

GLN

ILE

VAL

ARG

ASN

ASP

PRO

PRO

LEU

ARG

TYR

ASP

THR

ASN

LEU

PRO

VAL

ASP

LEU

LEU

HIS

MET

VAL

TYR

ALA

GLY

ARG

GLY

ALA

THR

GLY

SER

SER

GLY

VAL

VAL

PHE

GLY

THR

TRP

TYR

ARG

THR

ILE

GLN

ASP

ARG

THR

ILE

THR

ASP

PHE

PRO

LEU

THR

THR

ARG

SER

ALA

ASP

PHE

ARG

ASP

GLY

ARG

MET

SER

LYS

THR

PHE

MET

THR

ALA

LEU

VAL

LEU

SER

LEU

GLN

ALA

CYS

GLY

ARG

LEU

TYR

VAL

GLY

GLN

ARG

HIS

TYR

SER

ALA

PHE

GLU

CYS

ALA

VAL

LEU

CYS

LEU

TYR

LEU

LEU

TYR

ARG

ASN

THR

HIS

GLY

ALA

ALA

ASP

ASP

SER

ASP

ARG

ALA

PRO

VAL

THR

PHE

GLY

Page 28 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

ASP

LEU

LEU

GLY

ARG

LEU

PRO

ARG

TYR

LEU

ALA

CYS

LEU

ALA

ALA

VAL

ILE

GLY

THR

GLU

GLY

GLY

ARG

PRO

GLN

TYR

ARG

TYR

ARG

ASP

ASP

LYS

LEU

PRO

LYS

THR

GLN

PHE

ALA

ALA

GLY

GLY

GLY

ARG

TYR

GLU

HIS

GLY

ALA

LEU

ALA

SER

HIS

ILE

VAL

ILE

ALA

THR

LEU

MET

HIS

HIS

GLY

VAL

LEU

PRO

ALA

ALA

PRO

GLY

ASP

VAL

PRO

ARG

ASP

ALA

SER

THR

HIS

VAL

ASN

PRO

ASP

GLY

VAL

ALA

HIS

HIS

ASP

ASP

ILE

ASN

ARG

ALA

ALA

ALA

ALA

PHE

LEU

SER

ARG

GLY

HIS

ASN

LEU

PHE

LEU

TRP

GLU

ASP

GLN

THR

LEU

LEU

ARG

ALA

THR

ALA

ASN

THR

ILE

THR

ALA

LEU

GLY

VAL

ILE

GLN

ARG

LEU

LEU

ALA

ASN

GLY

ASN

VAL

TYR

ALA

ASP

ARG

LEU

ASN

ASN

ARG

LEU

GLN

LEU

GLY

MET

LEU

ILE

PRO

GLY

ALA

VAL

PRO

SER

GLU

ALA

ILE

ALA

ARG

GLY

ALA

SER

GLY

SER

ASP

SER

GLY

ALA

ILE

LYS

SER

GLY

ASP

ASN

ASN

LEU

GLU

ALA

LEU

CYS

ALA

ASN

TYR

VAL

LEU

PRO

LEU

TYR

ARG

ALA

ASP

PRO

ALA

VAL

GLU

LEU

THR

GLN

LEU

PHE

PRO

GLY

LEU

ALA

ALA

LEU

CYS

LEU

ASP

ALA

GLN

ALA

GLY

ARG

PRO

VAL

GLY

SER

THR

ARG

ARG

VAL

VAL

ASP

MET

SER

SER

GLY

ALA

ARG

GLN

ALA

ALA

LEU

VAL

ARG

LEU

THR

ALA

LEU

GLU

LEU

ILE

ASN

ARG

THR

ARG

THR

ASN

PRO

THR

PRO

VAL

GLY

GLU

VAL

ILE

HIS

ALA

HIS

ASP

ALA

LEU

ALA

ILE

GLN

TYR

GLU

GLN

GLY

LEU

GLY

LEU

LEU

ALA

GLN

GLN

ALA

ARG

ILE

GLY

LEU

GLY

SER

ASN

THR

LYS

ARG

PHE

SER

ALA

PHE

ASN

VAL

SER

SER

ASP

TYR

ASP

MET

LEU

TYR

PHE

LEU

CYS

LEU

GLY

PHE

ILE

PRO

GLN

TYR

LEU

SER

ALA

VAL

• Molecule 6: Capsid vertex component 2

Chain m:

MET

ASP

PRO

TYR

CYS

PRO

PHE

ASP

ALA

LEU

ASP

VAL

W13

�E14

�H15

R16

�R17

�

A21

�D22

�S23

R24

�

E30

�

R33

�D34

�F35

�W36

M37

�S38

�

N42

�

R45

�E46

�T47

�A48

�A49

�E50

�Q51

�

L55

�Q56

�A57

�

T60

�A61

A62

�A63

�A64

�

E67

�N68

�A69

�A70

�M71

�Q72

�A73

A74

�

E75�

L76�

P77

V78�

D79�

I80�

E81�

R82�

R83�

L84�

R85�

P86�

I87�

E88�

R89�

N90�

V91

H92�

GLU

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ALA

GLY

ALA

LEU

GLU

ALA

LEU

GLU

THR

ALA

ALA

ALA

ALA

ALA

GLU

GLU

ALA

ASP

ALA

ALA

ARG

GLY

ASP

GLU

PRO

ALA

GLY

GLY

GLY

ASP

GLY

GLY

ALA

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PRO

GLY

LEU

ALA

VAL

ALA

GLU

MET

GLU

VAL

GLN

ILE

VAL

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ASN

ASP

PRO

PRO

LEU

ARG

TYR

ASP

THR

ASN

LEU

PRO

VAL

ASP

LEU

LEU

HIS

MET

VAL

TYR

ALA

GLY

ARG

GLY

ALA

THR

GLY

SER

SER

GLY

VAL

VAL

PHE

GLY

THR

TRP

TYR

ARG

THR

ILE

GLN

ASP

ARG

THR

ILE

THR

ASP

PHE

PRO

LEU

THR

THR

ARG

SER

ALA

ASP

PHE

ARG

ASP

GLY

ARG

MET

SER

LYS

THR

PHE

MET

THR

ALA

LEU

VAL

LEU

SER

LEU

GLN

ALA

CYS

GLY

ARG

LEU

TYR

VAL

GLY

GLN

ARG

HIS

TYR

SER

ALA

PHE

GLU

CYS

ALA

VAL

LEU

CYS

LEU

TYR

LEU

LEU

TYR

ARG

ASN

THR

HIS

GLY

ALA

ALA

ASP

ASP

SER

ASP

ARG

ALA

PRO

VAL

THR

PHE

GLY

ASP

LEU

LEU

GLY

ARG

LEU

PRO

ARG

TYR

LEU

ALA

CYS

LEU

ALA

ALA

VAL

ILE

GLY

THR

GLU

GLY

GLY

ARG

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GLN

TYR

ARG

TYR

ARG

ASP

ASP

LYS

LEU

PRO

LYS

THR

GLN

PHE

ALA

ALA

GLY

GLY

GLY

ARG

TYR

GLU

HIS

GLY

ALA

LEU

ALA

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HIS

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VAL

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ALA

THR

LEU

MET

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HIS

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VAL

LEU

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ALA

ALA

PRO

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ASP

VAL

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ASP

ALA

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VAL

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ASP

GLY

VAL

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HIS

HIS

ASP

ASP

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ASN

ARG

ALA

ALA

ALA

ALA

PHE

LEU

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GLY

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ASN

LEU

PHE

LEU

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GLU

ASP

GLN

THR

LEU

LEU

ARG

ALA

THR

ALA

ASN

THR

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THR

ALA

LEU

GLY

VAL

ILE

GLN

ARG

LEU

LEU

ALA

ASN

GLY

ASN

VAL

TYR

ALA

ASP

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LEU

ASN

ASN

ARG

LEU

GLN

LEU

GLY

MET

LEU

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PRO

GLY

ALA

VAL

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GLU

ALA

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ALA

ARG

GLY

ALA

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GLY

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ASP

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GLY

ALA

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LYS

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GLY

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ASN

ASN

LEU

GLU

ALA

LEU

CYS

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TYR

VAL

LEU

PRO

LEU

TYR

ARG

ALA

ASP

PRO

ALA

VAL

GLU

LEU

THR

GLN

LEU

PHE

PRO

GLY

LEU

ALA

ALA

LEU

CYS

LEU

ASP

ALA

GLN

ALA

GLY

ARG

PRO

VAL

GLY

SER

THR

ARG

ARG

VAL

VAL

ASP

MET

SER

SER

GLY

ALA

ARG

GLN

ALA

ALA

LEU

VAL

ARG

LEU

THR

ALA

LEU

GLU

LEU

ILE

ASN

ARG

THR

ARG

THR

ASN

PRO

THR

PRO

VAL

GLY

GLU

VAL

ILE

HIS

ALA

HIS

ASP

ALA

LEU

ALA

ILE

GLN

TYR

GLU

GLN

GLY

LEU

GLY

LEU

LEU

ALA

GLN

GLN

ALA

ARG

ILE

GLY

LEU

GLY

SER

ASN

THR

LYS

ARG

PHE

SER

ALA

PHE

ASN

VAL

SER

SER

ASP

TYR

ASP

MET

LEU

TYR

PHE

LEU

CYS

LEU

GLY

PHE

ILE

PRO

GLN

TYR

LEU

SER

ALA

VAL

• Molecule 7: Large tegument protein deneddylase

Chain n:

Page 29 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

MET

ILE

ALA

GLY

THR

PRO

PRO

HIS

SER

THR

MET

GLU

ARG

GLY

GLY

ASP

ARG

ASP

ILE

VAL

VAL

THR

GLY

ALA

ARG

ASN

GLN

PHE

ALA

PRO

ASP

LEU

GLU

PRO

GLY

GLY

SER

VAL

SER

CYS

MET

ARG

SER

SER

LEU

SER

PHE

LEU

SER

LEU

ILE

PHE

ASP

VAL

GLY

PRO

ARG

ASP

VAL

LEU

SER

ALA

GLU

ALA

ILE

GLU

GLY

CYS

LEU

VAL

GLU

GLY

GLY

GLU

TRP

THR

ARG

ALA

THR

ALA

GLY

PRO

GLY

PRO

PRO

ARG

MET

CYS

SER

ILE

VAL

GLU

LEU

PRO

ASN

PHE

LEU

GLU

TYR

PRO

GLY

ALA

ARG

GLY

GLY

LEU

ARG

CYS

VAL

PHE

SER

ARG

VAL

TYR

GLY

GLU

VAL

GLY

PHE

PHE

GLY

GLU

PRO

ALA

ALA

GLY

LEU

LEU

GLU

THR

GLN

CYS

PRO

ALA

HIS

THR

PHE

PHE

ALA

GLY

PRO

TRP

ALA

LEU

ARG

PRO

LEU

SER

TYR

THR

LEU

LEU

THR

ILE

GLY

PRO

LEU

GLY

MET

GLY

LEU

PHE

ARG

ASP

GLY

ASP

THR

ALA

TYR

LEU

PHE

ASP

PRO

HIS

GLY

LEU

PRO

GLU

GLY

THR

PRO

ALA

PHE

ILE

ALA

LYS

VAL

ARG

ALA

GLY

ASP

MET

TYR

PRO

TYR

LEU

THR

TYR

TYR

THR

ARG

ASP

ARG

PRO

ASP

VAL

ARG

TRP

ALA

GLY

ALA

MET

VAL

PHE

PHE

VAL

PRO

SER

GLY

PRO

GLU

PRO

ALA

ALA

PRO

ALA

ASP

LEU

THR

ALA

ALA

ALA

LEU

HIS

LEU

TYR

GLY

ALA

SER

GLU

THR

TYR

LEU

GLN

ASP

GLU

ALA

PHE

SER

GLU

ARG

ARG

VAL

ALA

ILE

THR

HIS

PRO

LEU

ARG

GLY

GLU

ILE

ALA

GLY

LEU

GLY

GLU

PRO

CYS

VAL

GLY

VAL

GLY

PRO

ARG

GLU

GLY

VAL

GLY

GLY

PRO

GLY

PRO

HIS

PRO

PRO

THR

ALA

ALA

GLN

SER

PRO

PRO

PRO

THR

ARG

ALA

ARG

ARG

ASP

ASP

ARG

ALA

SER

GLU

THR

SER

ARG

GLY

THR

ALA

GLY

PRO

SER

ALA

LYS

PRO

GLU

ALA

LYS

ARG

PRO

ASN

ARG

ALA

PRO

ASP

ASP

VAL

TRP

ALA

VAL

ALA

LEU

LYS

GLY

THR

PRO

PRO

THR

ASP

PRO

PRO

SER

ALA

ASP

PRO

PRO

SER

ALA

ASP

PRO

PRO

SER

ALA

ILE

PRO

PRO

PRO

PRO

PRO

SER

ALA

PRO

LYS

THR

PRO

ALA

ALA

GLU

ALA

ALA

GLU

GLU

ASP

ASP

ASP

ASP

MET

ARG

VAL

LEU

GLU

MET

GLY

VAL

VAL

PRO

VAL

GLY

ARG

HIS

ARG

ALA

ARG

TYR

SER

ALA

GLY

LEU

PRO

LYS

ARG

ARG

ARG

PRO

THR

TRP

THR

PRO

PRO

SER

SER

VAL

GLU

ASP

LEU

THR

SER

GLY

GLU

LYS

THR

LYS

ARG

SER

ALA

PRO

PRO

ALA

LYS

THR

LYS

LYS

LYS

SER

THR

PRO

LYS

GLY

LYS

THR

PRO

VAL

GLY

ALA

ALA

VAL

PRO

ALA

SER

VAL

PRO

GLU

PRO

VAL

LEU

ALA

SER

ALA

PRO

PRO

ASP

PRO

ALA

GLY

PRO

PRO

VAL

ALA

GLU

ALA

GLY

GLU

ASP

ASP

GLY

PRO

THR

VAL

PRO

ALA

SER

SER

GLN

ALA

LEU

GLU

ALA

LEU

LYS

THR

ARG

ARG

SER

PRO

GLU

PRO

PRO

GLY

ALA

ASP

LEU

ALA

GLN

LEU

PHE

GLU

ALA

HIS

PRO

ASN

VAL

ALA

ALA

THR

ALA

VAL

LYS

PHE

THR

ALA

CYS

SER

ALA

ALA

LEU

ALA

ARG

GLU

VAL

ALA

ALA

CYS

SER

ARG

LEU

THR

ILE

SER

ALA

LEU

ARG

SER

PRO

TYR

PRO

ALA

SER

PRO

GLY

LEU

LEU

GLU

LEU

CYS

VAL

ILE

PHE

PHE

PHE

GLU

ARG

VAL

LEU

ALA

PHE

LEU

ILE

GLU

ASN

GLY

ALA

ARG

THR

HIS

THR

GLN

ALA

GLY

VAL

ALA

GLY

PRO

ALA

ALA

ALA

LEU

LEU

GLU

PHE

THR

LEU

ASN

MET

LEU

PRO

TRP

LYS

THR

ALA

VAL

GLY

ASP

PHE

LEU

ALA

SER

THR

ARG

LEU

SER

LEU

ALA

ASP

VAL

ALA

ALA

HIS

LEU

PRO

LEU

VAL

GLN

HIS

VAL

LEU

ASP

GLU

ASN

SER

LEU

ILE

GLY

ARG

LEU

ALA

LEU

ALA

LYS

LEU

ILE

LEU

VAL

ALA

ARG

ASP

VAL

ILE

ARG

GLU

THR

ASP

ALA

PHE

TYR

GLY

GLU

LEU

ALA

ASP

LEU

GLU

LEU

GLN

LEU

ARG

ALA

ALA

PRO

PRO

ALA

ASN

LEU

TYR

THR

ARG

LEU

GLY

GLU

TRP

LEU

LEU

GLU

ARG

SER

GLN

ALA

HIS

PRO

ASP

THR

LEU

PHE

ALA

PRO

ALA

THR

PRO

THR

HIS

PRO

GLU

PRO

LEU

LEU

TYR

ARG

VAL

GLN

ALA

LEU

ALA

LYS

PHE

ALA

ARG

GLY

GLU

GLU

ILE

ARG

VAL

GLU

ALA

GLU

ASP

ARG

GLN

MET

ARG

GLU

ALA

LEU

ASP

ALA

LEU

ALA

ARG

GLY

VAL

ASP

ALA

VAL

SER

GLN

HIS

ALA

GLY

PRO

LEU

GLY

VAL

MET

PRO

ALA

PRO

ALA

GLY

ALA

ALA

PRO

GLN

GLY

ALA

PRO

ARG

PRO

PRO

PRO

LEU

GLY

PRO

GLU

ALA

VAL

GLN

VAL

ARG

LEU

GLU

GLU

VAL

ARG

THR

GLN

ALA

ARG

ARG

ALA

ILE

GLU

GLY

ALA

VAL

LYS

GLU

TYR

PHE

TYR

ARG

GLY

ALA

VAL

TYR

SER

ALA

LYS

ALA

LEU

GLN

ALA

SER

ASP

ASN

ASN

ASP

ARG

ARG

PHE

HIS

VAL

ALA

SER

ALA

ALA

VAL

VAL

PRO

VAL

VAL

GLN

LEU

LEU

GLU

SER

LEU

PRO

VAL

PHE

ASP

GLN

HIS

THR

ARG

ASP

ILE

ALA

GLN

ARG

ALA

ALA

ILE

PRO

ALA

PRO

PRO

PRO

ILE

ALA

THR

SER

PRO

THR

ALA

ILE

LEU

LEU

ARG

ASP

LEU

ILE

GLN

ARG

GLY

GLN

THR

LEU

ASP

ALA

PRO

GLU

ASP

LEU

ALA

ALA

TRP

LEU

SER

VAL

LEU

THR

ASP

ALA

ALA

ASN

GLN

GLY

LEU

ILE

GLU

ARG

LYS

PRO

LEU

ASP

GLU

LEU

ALA

ARG

SER

ILE

ARG

ASP

ILE

ASN

ASP

GLN

GLN

ALA

ARG

ARG

SER

SER

GLY

LEU

ALA

GLU

LEU

ARG

ARG

PHE

ASP

ALA

LEU

ASP

ALA

ALA

LEU

GLY

GLN

GLN

LEU

ASP

SER

ASP

ALA

ALA

PHE

VAL

PRO

ALA

PRO

GLY

ALA

SER

PRO

TYR

PRO

ASP

ASP

GLY

GLY

LEU

SER

PRO

GLU

ALA

THR

ARG

MET

ALA

GLU

GLU

ALA

LEU

ARG

GLN

ALA

ARG

ALA

MET

ASP

ALA

ALA

LYS

LEU

THR

ALA

GLU

LEU

ALA

PRO

ASP

ALA

ARG

ALA

ARG

LEU

ARG

GLU

ARG

ALA

ARG

SER

LEU

GLU

ALA

MET

LEU

GLU

GLY

ALA

ARG

GLU

ARG

ALA

LYS

VAL

ALA

ARG

ASP

ALA

ARG

GLU

LYS

PHE

LEU

HIS

LYS

LEU

GLN

GLY

VAL

LEU

ARG

PRO

LEU

PRO

ASP

PHE

VAL

GLY

LEU

LYS

ALA

CYS

PRO

ALA

VAL

LEU

ALA

THR

LEU

ARG

ALA

SER

LEU

PRO

ALA

GLY

TRP

SER

ASP

LEU

PRO

GLU

ALA

VAL

ARG

GLY

ALA

PRO

PRO

GLU

VAL

THR

ALA

ALA

LEU

ARG

ALA

ASP

MET

TRP

GLY

LEU

LEU

GLY

GLN

TYR

ARG

ASP

ALA

LEU

GLU

HIS

PRO

THR

PRO

ASP

THR

ALA

THR

ALA

LEU

SER

GLY

LEU

HIS

PRO

SER

PHE

VAL

VAL

VAL

LEU

LYS

ASN

LEU

PHE

ALA

ASP

ALA

PRO

GLU

THR

PRO

PHE

LEU

LEU

GLN

PHE

PHE

ALA

ASP

HIS

ALA

PRO

ILE

ILE

ALA

HIS

ALA

VAL

SER

ASN

ALA

ILE

ASN

ALA

GLY

SER

ALA

ALA

VAL

ALA

THR

ALA

ASP

PRO

ALA

SER

THR

VAL

ASP

ALA

ALA

VAL

ARG

ALA

HIS

ARG

VAL

LEU

VAL

ASP

ALA

VAL

THR

ALA

LEU

GLY

ALA

ALA

ALA

SER

ASP

PRO

ALA

SER

PRO

LEU

ALA

PHE

LEU

ALA

ALA

MET

Page 30 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

ALA

ASP

SER

ALA

ALA

GLY

TYR

VAL

LYS

ALA

THR

ARG

LEU

ALA

LEU

ASP

ALA

ARG

VAL

ALA

ILE

ALA

GLN

LEU

THR

THR

LEU

GLY

SER

ALA

ALA

ALA

ASP

LEU

VAL

VAL

GLN

VAL

ARG

ARG

ALA

ALA

ASN

GLN

PRO

GLU

GLY

GLU

HIS

ALA

SER

LEU

ILE

GLN

ALA

ALA

THR

ARG

ALA

THR

THR

GLY

ALA

ARG

GLU

SER

LEU

ALA

GLY

HIS

GLU

GLY

ARG

PHE

GLY

GLY

LEU

LEU

HIS

ALA

GLU

GLY

THR

ALA

GLY

ASP

HIS

SER

PRO

SER

GLY

ARG

ALA

LEU

GLN

GLU

LEU

GLY

LYS

VAL

ILE

GLY

ALA

THR

ARG

ARG

ARG

ALA

ASP

GLU

LEU

GLU

ALA

ALA

THR

ALA

ASP

LEU

ARG

GLU

LYS

MET

ALA

ALA

GLN

ARG

ALA

ARG

SER

SER

HIS

GLU

ARG

TRP

ALA

ALA

ASP

VAL

GLU

ALA

VAL

LEU

ASP

ARG

VAL

GLU

SER

GLY

ALA

GLU

PHE

ASP

VAL

VAL

GLU

LEU

ARG

ARG

LEU

GLN

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ALA

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ASP

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ALA

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VAL

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LEU

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LEU

ALA

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ASN

PRO

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PRO

GLU

ASN

GLN

ARG

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PRO

MET

LEU

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PRO

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ALA

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ARG

ILE

ASP

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ALA

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ALA

ALA

ASP

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ASP

MET

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VAL

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GLU

PRO

LEU

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ARG

LEU

LEU

ARG

LEU

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GLY

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ARG

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ASP

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PRO

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VAL

ASP

ILE

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ASP

ARG

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ASP

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ARG

ALA

ASP

ALA

ARG

ARG

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VAL

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ALA

ALA

ALA

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ASP

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ALA

ALA

ALA

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VAL

ARG

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VAL

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PRO

CYS

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ASP

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VAL

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ASP

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ASP

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ASP

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ASP

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VAL

ARG

ALA

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GLN

ARG

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ALA

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GLU

ARG

VAL

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ARG

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VAL

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ALA

ARG

GLU

ARG

ARG

ALA

GLN

LEU

GLU

ALA

GLU

GLY

LEU

ALA

ASN

LEU

LYS

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LEU

LEU

LYS

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VAL

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PRO

ALA

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ASP

GLN

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ALA

ALA

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ASP

GLY

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GLY

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LEU

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GLN

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LEU

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ASP

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ARG

ARG

ARG

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GLU

ALA

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ARG

ARG

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GLU

GLU

ALA

GLU

ALA

GLU

TRP

ASP

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VAL

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ARG

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GLY

ARG

VAL

ARG

GLY

GLY

ALA

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GLU

GLY

PHE

ARG

ALA

ALA

CYS

GLU

GLN

LEU

ARG

ALA

LEU

GLN

ASP

THR

THR

ASN

THR

VAL

SER

GLY

LEU

ARG

ALA

GLN

ARG

ASP

TYR

GLU

ARG

LEU

PRO

ALA

LYS

TYR

GLN

GLY

VAL

LEU

GLY

ALA

LYS

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ALA

GLU

ARG

ALA

GLY

ALA

VAL

GLU

GLU

LEU

GLY

GLY

ARG

VAL

ALA

GLN

HIS

ALA

ASP

LEU

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ALA

ARG

LEU

ARG

ASP

GLU

VAL

VAL

PRO

ARG

VAL

ALA

TRP

GLU

MET

ASN

PHE

ASP

THR

LEU

GLY

GLY

LEU

LEU

ALA

GLU

PHE

ASP

ALA

VAL

ALA

GLY

ASP

LEU

ALA

PRO

TRP

ALA

VAL

GLU

GLU

PHE

ARG

GLY

ALA

ARG

GLU

LEU

ILE

GLN

ARG

ARG

MET

GLY

LEU

TYR

SER

ALA

TYR

ALA

LYS

ALA

THR

GLY

GLN

THR

GLY

ALA

GLY

ALA

ALA

ALA

ALA

PRO

ALA

PRO

LEU

LEU

VAL

ASP

LEU

ARG

ALA

LEU

ASP

ALA

ARG

ALA

ARG

ALA

SER

ALA

PRO

PRO

GLY

GLN

GLU

ALA

ASP

PRO

GLN

MET

LEU

ARG

ARG

ARG

GLY

GLU

ALA

TYR

LEU

ARG

VAL

SER

GLY

GLY

PRO

GLY

PRO

LEU

VAL

LEU

ARG

GLU

ALA

THR

SER

THR

LEU

ASP

ARG

PRO

PHE

ALA

PRO

SER

PHE

LEU

VAL

PRO

ASP

GLY

THR

PRO

LEU

GLN

TYR

ALA

LEU

CYS

PHE

PRO

ALA

VAL

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ASP

LYS

LEU

GLY

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LEU

LEU

MET

CYS

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GLU

ALA

ALA

CYS

ILE

ARG

PRO

PRO

LEU

PRO

THR

ASP

THR

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GLU

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ALA

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THR

VAL

THR

ALA

MET

TYR

VAL

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THR

VAL

ILE

ASN

ARG

LEU

GLN

LEU

ALA

LEU

SER

ASP

ALA

GLN

ALA

ALA

ASN

PHE

GLN

LEU

PHE

GLY

ARG

PHE

VAL

ARG

HIS

ARG

GLN

ALA

ARG

TRP

GLY

ALA

SER

MET

ASP

ALA

ALA

ALA

GLU

LEU

TYR

VAL

ALA

LEU

VAL

ALA

THR

THR

LEU

THR

ARG

GLU

PHE

GLY

CYS

ARG

TRP

ALA

GLN

LEU

GLU

TRP

GLY

GLY

ASP

ALA

ALA

ALA

PRO

GLY

PRO

PRO

LEU

GLY

PRO

GLN

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THR

ARG

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ARG

VAL

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PHE

ASN

GLU

ASN

ASP

VAL

LEU

VAL

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PRO

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TYR

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ARG

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ASP

LEU

VAL

ARG

GLN

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MET

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LEU

THR

LEU

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ARG

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GLN

ASN

ALA

ALA

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VAL

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ARG

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PRO

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ALA

ARG

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VAL

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GLY

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ARG

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LYS

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VAL

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MET

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PRO

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PHE

PRO

ASP

ASP

TYR

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ASP

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ASP

ALA

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LEU

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ALA

ARG

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GLU

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GLN

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LEU

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PRO

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GLY

ARG

GLU

ALA

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PRO

PRO

ALA

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LEU

TYR

ARG

PRO

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GLN

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VAL

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VAL

PRO

ALA

ALA

ALA

THR

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ARG

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PRO

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ALA

ARG

VAL

THR

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MET

ASP

LEU

VAL

LEU

ALA

ALA

VAL

LEU

LEU

GLY

ALA

PRO

VAL

VAL

VAL

ALA

LEU

ARG

ASN

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THR

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ARG

GLU

SER

GLU

LEU

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CYS

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ARG

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ASP

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VAL

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ASP

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VAL

ARG

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LEU

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PRO

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ASN

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CYS

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ALA

GLN

LEU

PRO

ARG

LEU

SER

ALA

Page 31 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

LEU

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ALA

GLU

ARG

PRO

LEU

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PRO

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ARG

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GLN

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GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

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GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

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GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

GLN

PRO

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GLN

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GLN

PRO

GLN

PRO

GLN

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GLN

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GLN

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GLN

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GLN

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ALA

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Q3092�

R3093�

T3094�

G3095�

R3096�

S3097�

A3098�

L3099�

A3100�

V3101�

L3102�

I3103�

R3104�

A3105�

C3106�

Y3107�

R3108�

L3109�

Q3110�

Q3111�

Q3112�

L3113�

Q3114�

R3115�

T3116�

R3117�

R3118�

A3119�

L3120�

L3121�

H3122�

H3123�

S3124�

D3125�

A3126�

V3127

L3128�

T3129�

S3130�

L3131�

H3132�

H3133�

V3134

R3135�

M3136�

L3137�

L3138�

GLY

• Molecule 7: Large tegument protein deneddylase

Chain o:

MET

ILE

ALA

GLY

THR

PRO

PRO

HIS

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THR

MET

GLU

ARG

GLY

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ASP

ARG

ASP

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VAL

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ARG

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VAL

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VAL

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GLY

GLU

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THR

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ALA

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GLY

PRO

PRO

ARG

MET

CYS

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ILE

VAL

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LEU

PRO

ASN

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GLU

TYR

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GLY

GLY

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CYS

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VAL

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ALA

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ASP

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PRO

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ARG

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ARG

ARG

Page 32 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

ASP

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ALA

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GLU

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Page 33 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

ILE

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Page 34 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

PRO

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Page 35 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

4 Experimental information iO

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, I DepositorNumber of particles used 28042 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE

CORRECTIONDepositor

Microscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å

2) 25 Depositor

Minimum defocus (nm) 2000 DepositorMaximum defocus (nm) 2000 DepositorMagni�cation 24271 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 14.209 DepositorMinimum map value -10.389 DepositorAverage map value -0.000 DepositorMap value standard deviation 0.999 DepositorRecommended contour level 2.5 DepositorMap size (Å) 1318.3999, 1318.3999, 1318.3999 DepositorMap dimensions 1280, 1280, 1280 DepositorMap angles (◦) 90.0, 90.0, 90.0 DepositorPixel spacing (Å) 1.03, 1.03, 1.03 Depositor

Page 36 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

5 Model quality iO

5.1 Standard geometry iO

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol ChainBond lengths Bond angles

RMSZ #|Z| >5 RMSZ #|Z| >51 4 0.34 0/9878 0.57 3/13478 (0.0%)1 A 0.36 0/10664 0.58 3/14556 (0.0%)1 B 0.37 0/10680 0.59 1/14579 (0.0%)1 C 0.37 1/10680 (0.0%) 0.58 3/14579 (0.0%)1 D 0.39 0/10664 0.60 3/14556 (0.0%)1 E 0.39 0/10699 0.60 2/14605 (0.0%)1 F 0.38 0/10664 0.59 1/14556 (0.0%)1 M 0.38 0/10664 0.60 1/14556 (0.0%)1 N 0.39 0/10699 0.59 0/146051 O 0.37 0/10680 0.58 0/145791 S 0.36 0/10616 0.58 2/14487 (0.0%)1 T 0.38 0/10631 0.60 2/14507 (0.0%)1 U 0.39 1/10680 (0.0%) 0.60 1/14579 (0.0%)1 V 0.37 0/10664 0.59 3/14556 (0.0%)1 W 0.37 0/10680 0.58 0/145791 X 0.37 0/10567 0.59 3/14423 (0.0%)2 0 0.31 0/796 0.48 0/10872 1 0.31 0/796 0.48 0/10872 2 0.31 0/796 0.48 0/10872 3 0.31 0/796 0.48 0/10872 G 0.31 0/796 0.48 0/10872 H 0.31 0/796 0.48 0/10872 I 0.31 0/796 0.48 0/10872 J 0.31 0/796 0.48 0/10872 K 0.31 0/796 0.48 0/10872 L 0.31 0/796 0.48 0/10872 P 0.31 0/796 0.48 0/10872 Q 0.31 0/796 0.48 0/10872 R 0.31 0/796 0.48 0/10872 Y 0.31 0/796 0.48 0/10872 Z 0.31 0/796 0.48 0/10873 5 0.38 1/2795 (0.0%) 0.57 0/38103 8 0.37 0/2858 0.59 1/3895 (0.0%)3 b 0.37 0/2858 0.58 0/3895

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Mol ChainBond lengths Bond angles

RMSZ #|Z| >5 RMSZ #|Z| >53 e 0.35 0/2791 0.57 0/38053 h 0.35 0/2795 0.59 1/3810 (0.0%)4 6 0.36 0/2152 0.62 1/2939 (0.0%)4 7 0.36 0/2383 0.66 2/3259 (0.1%)4 9 0.36 0/2127 0.62 0/29064 a 0.38 0/2383 0.68 3/3259 (0.1%)4 c 0.36 0/2127 0.64 1/2906 (0.0%)4 d 0.38 0/2383 0.67 3/3259 (0.1%)4 f 0.36 0/2124 0.63 2/2900 (0.1%)4 g 0.37 0/2383 0.63 2/3259 (0.1%)4 i 0.35 0/2152 0.60 1/2939 (0.0%)4 j 0.36 0/2383 0.65 2/3259 (0.1%)5 k 0.33 0/4307 0.54 0/58666 l 0.33 0/786 0.52 0/10726 m 0.34 0/670 0.57 1/912 (0.1%)7 n 0.22 0/388 0.40 0/5217 o 0.22 0/388 0.40 0/521All All 0.37 3/224983 (0.0%) 0.59 48/307077 (0.0%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers1 4 0 21 A 0 21 B 0 21 C 0 11 D 0 21 E 0 11 F 0 21 M 0 21 N 0 21 O 0 11 S 0 11 T 0 21 U 0 51 V 0 31 W 0 41 X 0 13 8 0 1

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Mol Chain #Chirality outliers #Planarity outliers3 h 0 14 7 0 14 9 0 14 a 0 14 d 0 14 g 0 14 j 0 1All All 0 41

All (3) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 5 315 TYR CD1-CE1 -6.41 1.29 1.391 C 954 TYR CD1-CE1 -6.12 1.30 1.391 U 11 TYR CD2-CE2 -5.88 1.30 1.39

All (48) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 T 159 LEU CB-CG-CD1 -8.25 96.97 111.004 j 63 LEU CA-CB-CG 7.91 133.48 115.304 a 63 LEU CA-CB-CG 7.26 132.00 115.306 m 55 LEU CA-CB-CG 7.17 131.79 115.304 7 63 LEU CA-CB-CG 7.08 131.58 115.301 D 745 ARG NE-CZ-NH1 -7.07 116.77 120.301 V 159 LEU CA-CB-CG -6.97 99.27 115.301 B 159 LEU CA-CB-CG -6.90 99.42 115.301 E 159 LEU CB-CG-CD1 -6.77 99.48 111.003 h 259 LEU CA-CB-CG 6.74 130.79 115.304 a 39 ARG NE-CZ-NH2 -6.64 116.98 120.301 4 195 LEU CA-CB-CG 6.62 130.52 115.301 C 159 LEU CA-CB-CG -6.58 100.17 115.304 d 69 ARG NE-CZ-NH1 -6.54 117.03 120.301 A 159 LEU CB-CG-CD1 -6.32 100.27 111.001 E 27 ILE CG1-CB-CG2 -6.29 97.57 111.401 X 311 LEU CA-CB-CG 5.94 128.96 115.304 d 63 LEU CA-CB-CG 5.93 128.93 115.301 U 406 LEU CA-CB-CG 5.80 128.64 115.304 6 202 LEU CA-CB-CG 5.65 128.29 115.304 g 63 LEU CA-CB-CG 5.60 128.19 115.304 d 37 ILE CG1-CB-CG2 -5.57 99.15 111.401 V 103 LEU CA-CB-CG 5.55 128.06 115.30

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Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 8 259 LEU CA-CB-CG 5.54 128.03 115.301 M 745 ARG NE-CZ-NH1 -5.53 117.53 120.304 f 202 LEU CA-CB-CG 5.53 128.01 115.301 X 195 LEU CA-CB-CG 5.49 127.93 115.301 A 1102 LEU CA-CB-CG 5.48 127.91 115.301 T 195 LEU CA-CB-CG 5.42 127.77 115.301 S 1369 LEU CA-CB-CG 5.41 127.75 115.301 X 41 ARG NE-CZ-NH2 -5.35 117.63 120.301 F 103 LEU CA-CB-CG 5.34 127.58 115.301 S 195 LEU CA-CB-CG 5.34 127.58 115.304 g 37 ILE CG1-CB-CG2 -5.33 99.68 111.401 D 103 LEU CA-CB-CG 5.28 127.44 115.301 V 1102 LEU CA-CB-CG 5.27 127.42 115.304 7 37 ILE CG1-CB-CG2 -5.27 99.81 111.401 A 406 LEU CA-CB-CG 5.26 127.39 115.301 4 406 LEU CA-CB-CG 5.22 127.31 115.304 f 18 ARG NE-CZ-NH1 5.22 122.91 120.301 4 344 LEU CA-CB-CG 5.16 127.17 115.301 C 103 LEU CA-CB-CG 5.12 127.07 115.304 c 18 ARG NE-CZ-NH1 5.11 122.85 120.301 D 1102 LEU CA-CB-CG 5.11 127.04 115.304 a 39 ARG CG-CD-NE -5.06 101.17 111.804 i 202 LEU CA-CB-CG 5.01 126.82 115.301 C 406 LEU CA-CB-CG 5.00 126.81 115.304 j 37 ILE CG1-CB-CG2 -5.00 100.39 111.40

There are no chirality outliers.

All (41) planarity outliers are listed below:

Mol Chain Res Type Group1 4 112 ILE Peptide1 4 64 THR Peptide4 7 241 LEU Peptide3 8 281 PRO Peptide4 9 96 GLY Peptide1 A 133 PHE Peptide1 A 800 HIS Peptide1 B 133 PHE Peptide1 B 43 ARG Peptide1 C 133 PHE Peptide1 D 622 ASN Peptide1 D 800 HIS Peptide

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Mol Chain Res Type Group1 E 133 PHE Peptide1 F 133 PHE Peptide1 F 622 ASN Peptide1 M 133 PHE Peptide1 M 43 ARG Peptide1 N 133 PHE Peptide1 N 800 HIS Peptide1 O 133 PHE Peptide1 S 133 PHE Peptide1 T 133 PHE Peptide1 T 800 HIS Peptide1 U 133 PHE Peptide1 U 43 ARG Peptide1 U 44 SER Peptide1 U 54 PHE Peptide1 U 622 ASN Peptide1 V 133 PHE Peptide1 V 159 LEU Peptide1 V 800 HIS Peptide1 W 133 PHE Peptide1 W 43 ARG Peptide1 W 622 ASN Peptide1 W 800 HIS Peptide1 X 133 PHE Peptide4 a 241 LEU Peptide4 d 241 LEU Peptide4 g 241 LEU Peptide3 h 281 PRO Peptide4 j 241 LEU Peptide

5.2 Too-close contacts iO

Due to software issues we are unable to calculate clashes - this section is therefore empty.

5.3 Torsion angles iO

5.3.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

Page 41 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 4 1243/1374 (90%) 1169 (94%) 74 (6%) 0 100 100

1 A 1358/1374 (99%) 1262 (93%) 96 (7%) 0 100 100

1 B 1360/1374 (99%) 1258 (92%) 102 (8%) 0 100 100

1 C 1360/1374 (99%) 1265 (93%) 95 (7%) 0 100 100

1 D 1358/1374 (99%) 1246 (92%) 112 (8%) 0 100 100

1 E 1362/1374 (99%) 1254 (92%) 108 (8%) 0 100 100

1 F 1358/1374 (99%) 1244 (92%) 114 (8%) 0 100 100

1 M 1358/1374 (99%) 1244 (92%) 114 (8%) 0 100 100

1 N 1362/1374 (99%) 1253 (92%) 108 (8%) 1 (0%) 51 85

1 O 1360/1374 (99%) 1260 (93%) 100 (7%) 0 100 100

1 S 1353/1374 (98%) 1272 (94%) 81 (6%) 0 100 100

1 T 1349/1374 (98%) 1272 (94%) 77 (6%) 0 100 100

1 U 1360/1374 (99%) 1244 (92%) 116 (8%) 0 100 100

1 V 1358/1374 (99%) 1247 (92%) 111 (8%) 0 100 100

1 W 1360/1374 (99%) 1252 (92%) 108 (8%) 0 100 100

1 X 1344/1374 (98%) 1260 (94%) 84 (6%) 0 100 100

2 0 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 1 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 2 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 3 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 G 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 H 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 I 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 J 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 K 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 L 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 P 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 Q 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 R 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

2 Y 99/112 (88%) 94 (95%) 5 (5%) 0 100 100Continued on next page...

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Mol Chain Analysed Favoured Allowed Outliers Percentiles

2 Z 99/112 (88%) 94 (95%) 5 (5%) 0 100 100

3 5 349/465 (75%) 332 (95%) 17 (5%) 0 100 100

3 8 361/465 (78%) 340 (94%) 20 (6%) 1 (0%) 41 76

3 b 361/465 (78%) 341 (94%) 20 (6%) 0 100 100

3 e 348/465 (75%) 324 (93%) 24 (7%) 0 100 100

3 h 349/465 (75%) 326 (93%) 22 (6%) 1 (0%) 41 76

4 6 264/318 (83%) 249 (94%) 15 (6%) 0 100 100

4 7 304/318 (96%) 283 (93%) 19 (6%) 2 (1%) 22 62

4 9 264/318 (83%) 244 (92%) 20 (8%) 0 100 100

4 a 304/318 (96%) 277 (91%) 25 (8%) 2 (1%) 22 62

4 c 264/318 (83%) 246 (93%) 17 (6%) 1 (0%) 34 72

4 d 304/318 (96%) 274 (90%) 27 (9%) 3 (1%) 15 54

4 f 260/318 (82%) 238 (92%) 21 (8%) 1 (0%) 34 72

4 g 304/318 (96%) 276 (91%) 28 (9%) 0 100 100

4 i 264/318 (83%) 246 (93%) 18 (7%) 0 100 100

4 j 304/318 (96%) 273 (90%) 30 (10%) 1 (0%) 41 76

5 k 534/703 (76%) 514 (96%) 20 (4%) 0 100 100

6 l 92/580 (16%) 87 (95%) 5 (5%) 0 100 100

6 m 78/580 (13%) 77 (99%) 1 (1%) 0 100 100

7 n 45/3139 (1%) 45 (100%) 0 0 100 100

7 o 45/3139 (1%) 45 (100%) 0 0 100 100

All All 28486/37310 (76%) 26449 (93%) 2024 (7%) 13 (0%) 100 100

All (13) Ramachandran outliers are listed below:

Mol Chain Res Type3 8 282 ARG4 7 241 LEU4 d 241 LEU4 d 242 GLN3 h 282 ARG1 N 8 PRO4 7 242 GLN4 a 241 LEU4 a 242 GLN

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Mol Chain Res Type4 f 76 THR4 j 241 LEU4 d 55 GLY4 c 35 PRO

5.3.2 Protein sidechains iO

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 4 1003/1085 (92%) 1002 (100%) 1 (0%) 93 97

1 A 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97

1 B 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97

1 C 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97

1 D 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97

1 E 1080/1085 (100%) 1079 (100%) 1 (0%) 93 97

1 F 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97

1 M 1076/1085 (99%) 1074 (100%) 2 (0%) 93 96

1 N 1080/1085 (100%) 1078 (100%) 2 (0%) 93 96

1 O 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97

1 S 1070/1085 (99%) 1069 (100%) 1 (0%) 93 97

1 T 1073/1085 (99%) 1072 (100%) 1 (0%) 93 97

1 U 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97

1 V 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97

1 W 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97

1 X 1069/1085 (98%) 1067 (100%) 2 (0%) 93 96

2 0 80/89 (90%) 80 (100%) 0 100 100

2 1 80/89 (90%) 80 (100%) 0 100 100

2 2 80/89 (90%) 80 (100%) 0 100 100

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Mol Chain Analysed Rotameric Outliers Percentiles

2 G 80/89 (90%) 80 (100%) 0 100 100

2 H 80/89 (90%) 80 (100%) 0 100 100

2 I 80/89 (90%) 80 (100%) 0 100 100

2 J 80/89 (90%) 80 (100%) 0 100 100

2 K 80/89 (90%) 80 (100%) 0 100 100

2 L 80/89 (90%) 80 (100%) 0 100 100

2 P 80/89 (90%) 80 (100%) 0 100 100

2 Q 80/89 (90%) 80 (100%) 0 100 100

2 R 80/89 (90%) 80 (100%) 0 100 100

2 Y 80/89 (90%) 80 (100%) 0 100 100

2 Z 80/89 (90%) 80 (100%) 0 100 100

3 5 279/364 (77%) 279 (100%) 0 100 100

3 8 285/364 (78%) 285 (100%) 0 100 100

3 b 285/364 (78%) 285 (100%) 0 100 100

3 e 279/364 (77%) 279 (100%) 0 100 100

3 h 279/364 (77%) 279 (100%) 0 100 100

4 6 234/264 (89%) 234 (100%) 0 100 100

4 7 256/264 (97%) 256 (100%) 0 100 100

4 9 231/264 (88%) 231 (100%) 0 100 100

4 a 256/264 (97%) 256 (100%) 0 100 100

4 c 231/264 (88%) 231 (100%) 0 100 100

4 d 256/264 (97%) 255 (100%) 1 (0%) 91 94

4 f 231/264 (88%) 231 (100%) 0 100 100

4 g 256/264 (97%) 256 (100%) 0 100 100

4 i 234/264 (89%) 234 (100%) 0 100 100

4 j 256/264 (97%) 256 (100%) 0 100 100

5 k 429/529 (81%) 428 (100%) 1 (0%) 93 96

6 l 80/448 (18%) 80 (100%) 0 100 100

6 m 67/448 (15%) 66 (98%) 1 (2%) 65 80

7 n 41/2430 (2%) 40 (98%) 1 (2%) 49 69

7 o 41/2430 (2%) 40 (98%) 1 (2%) 49 69Continued on next page...

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Mol Chain Analysed Rotameric Outliers Percentiles

All All 22851/29440 (78%) 22827 (100%) 24 (0%) 93 97

All (24) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 519 ARG1 B 519 ARG1 C 519 ARG1 D 519 ARG1 E 519 ARG1 F 519 ARG1 M 272 ARG1 M 519 ARG1 N 519 ARG1 N 558 LEU1 O 519 ARG1 S 519 ARG1 T 519 ARG1 U 519 ARG1 V 519 ARG1 W 519 ARG1 X 451 ARG1 X 519 ARG1 4 519 ARG4 d 77 ARG5 k 103 ARG6 m 82 ARG7 n 3115 ARG7 o 3115 ARG

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (345) suchsidechains are listed below:

Mol Chain Res Type1 A 63 ASN1 A 164 GLN1 A 168 ASN1 A 266 HIS1 A 429 HIS1 A 456 HIS1 A 485 ASN1 A 723 ASN

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Mol Chain Res Type1 A 777 ASN1 A 808 HIS1 A 863 HIS1 A 895 GLN1 A 961 HIS1 A 969 HIS1 A 1004 GLN1 A 1037 HIS1 A 1039 GLN1 A 1127 GLN1 A 1128 ASN1 A 1248 GLN1 B 63 ASN1 B 91 ASN1 B 164 GLN1 B 168 ASN1 B 266 HIS1 B 429 HIS1 B 456 HIS1 B 502 GLN1 B 717 GLN1 B 723 ASN1 B 782 GLN1 B 808 HIS1 B 863 HIS1 B 866 HIS1 B 961 HIS1 B 969 HIS1 B 1009 HIS1 B 1037 HIS1 B 1039 GLN1 C 63 ASN1 C 429 HIS1 C 456 HIS1 C 657 ASN1 C 658 ASN1 C 777 ASN1 C 788 GLN1 C 841 ASN1 C 866 HIS1 C 961 HIS1 C 1009 HIS

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Mol Chain Res Type1 C 1037 HIS1 C 1128 ASN1 C 1248 GLN1 C 1258 ASN1 C 1286 HIS1 D 91 ASN1 D 164 GLN1 D 168 ASN1 D 266 HIS1 D 315 ASN1 D 429 HIS1 D 456 HIS1 D 502 GLN1 D 503 GLN1 D 604 HIS1 D 696 HIS1 D 723 ASN1 D 724 HIS1 D 777 ASN1 D 788 GLN1 D 808 HIS1 D 841 ASN1 D 863 HIS1 D 969 HIS1 D 972 ASN1 D 1009 HIS1 D 1039 GLN1 D 1127 GLN1 D 1248 GLN1 D 1262 HIS1 E 164 GLN1 E 168 ASN1 E 266 HIS1 E 429 HIS1 E 456 HIS1 E 485 ASN1 E 502 GLN1 E 658 ASN1 E 785 HIS1 E 863 HIS1 E 969 HIS1 E 1009 HIS

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Mol Chain Res Type1 E 1037 HIS1 E 1117 ASN1 E 1127 GLN1 E 1128 ASN1 E 1248 GLN1 F 47 ASN1 F 63 ASN1 F 118 ASN1 F 456 HIS1 F 723 ASN1 F 863 HIS1 F 961 HIS1 F 1009 HIS1 F 1039 GLN1 F 1117 ASN1 F 1127 GLN1 F 1128 ASN1 F 1248 GLN2 J 57 GLN1 M 32 HIS1 M 266 HIS1 M 429 HIS1 M 456 HIS1 M 485 ASN1 M 658 ASN1 M 723 ASN1 M 785 HIS1 M 841 ASN1 M 863 HIS1 M 961 HIS1 M 969 HIS1 M 1009 HIS1 M 1037 HIS1 M 1039 GLN1 M 1083 HIS1 M 1090 ASN1 M 1127 GLN1 M 1128 ASN1 M 1248 GLN1 N 32 HIS1 N 63 ASN1 N 164 GLN

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Mol Chain Res Type1 N 168 ASN1 N 266 HIS1 N 315 ASN1 N 429 HIS1 N 456 HIS1 N 502 GLN1 N 723 ASN1 N 724 HIS1 N 777 ASN1 N 785 HIS1 N 808 HIS1 N 863 HIS1 N 961 HIS1 N 969 HIS1 N 1037 HIS1 N 1039 GLN1 N 1083 HIS1 N 1128 ASN1 O 266 HIS1 O 456 HIS1 O 502 GLN1 O 515 HIS1 O 658 ASN1 O 717 GLN1 O 723 ASN1 O 777 ASN1 O 866 HIS1 O 876 ASN1 O 961 HIS1 O 969 HIS1 O 1004 GLN1 O 1037 HIS1 O 1039 GLN1 O 1127 GLN1 O 1248 GLN1 S 100 HIS1 S 130 ASN1 S 156 HIS1 S 164 GLN1 S 168 ASN1 S 186 HIS1 S 266 HIS

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Mol Chain Res Type1 S 456 HIS1 S 515 HIS1 S 717 GLN1 S 723 ASN1 S 724 HIS1 S 863 HIS1 S 866 HIS1 S 961 HIS1 S 969 HIS1 S 1004 GLN1 S 1037 HIS1 S 1039 GLN1 S 1258 ASN1 T 63 ASN1 T 118 ASN1 T 156 HIS1 T 163 GLN1 T 164 GLN1 T 168 ASN1 T 266 HIS1 T 456 HIS1 T 717 GLN1 T 723 ASN1 T 724 HIS1 T 777 ASN1 T 788 GLN1 T 863 HIS1 T 866 HIS1 T 961 HIS1 T 969 HIS1 T 1004 GLN1 T 1037 HIS1 T 1039 GLN1 T 1090 ASN1 T 1128 ASN1 U 63 ASN1 U 163 GLN1 U 164 GLN1 U 168 ASN1 U 429 HIS1 U 456 HIS1 U 639 HIS

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Mol Chain Res Type1 U 717 GLN1 U 723 ASN1 U 777 ASN1 U 785 HIS1 U 808 HIS1 U 841 ASN1 U 863 HIS1 U 866 HIS1 U 895 GLN1 U 899 HIS1 U 900 ASN1 U 969 HIS1 U 1037 HIS1 U 1039 GLN1 V 63 ASN1 V 163 GLN1 V 164 GLN1 V 168 ASN1 V 266 HIS1 V 456 HIS1 V 502 GLN1 V 658 ASN1 V 723 ASN1 V 782 GLN1 V 841 ASN1 V 863 HIS1 V 866 HIS1 V 961 HIS1 V 969 HIS1 V 1004 GLN1 V 1009 HIS1 V 1037 HIS1 V 1039 GLN1 V 1127 GLN1 V 1248 GLN1 W 156 HIS1 W 266 HIS1 W 456 HIS1 W 723 ASN1 W 788 GLN1 W 808 HIS1 W 863 HIS

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Mol Chain Res Type1 W 866 HIS1 W 961 HIS1 W 969 HIS1 W 1009 HIS1 W 1037 HIS1 W 1039 GLN1 W 1127 GLN1 X 266 HIS1 X 429 HIS1 X 456 HIS1 X 658 ASN1 X 717 GLN1 X 723 ASN1 X 724 HIS1 X 777 ASN1 X 863 HIS1 X 866 HIS1 X 961 HIS1 X 969 HIS1 X 1004 GLN1 X 1037 HIS1 X 1039 GLN1 X 1117 ASN1 X 1128 ASN1 X 1262 HIS2 Y 68 HIS2 Z 68 HIS2 1 68 HIS1 4 100 HIS1 4 117 HIS1 4 186 HIS1 4 266 HIS1 4 340 GLN1 4 456 HIS1 4 515 HIS1 4 658 ASN1 4 717 GLN1 4 724 HIS1 4 785 HIS1 4 961 HIS1 4 969 HIS1 4 1004 GLN

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Mol Chain Res Type1 4 1009 HIS1 4 1037 HIS1 4 1258 ASN3 5 145 GLN3 5 235 HIS3 5 356 HIS4 6 281 HIS4 7 40 GLN4 7 193 GLN4 7 281 HIS3 8 120 GLN3 8 135 HIS3 8 356 HIS4 a 193 GLN4 a 242 GLN3 b 120 GLN3 b 135 HIS3 b 235 HIS3 b 237 HIS3 b 356 HIS3 b 369 ASN3 b 393 ASN4 d 193 GLN4 d 208 ASN3 e 120 GLN3 e 369 ASN4 f 238 ASN4 f 281 HIS4 g 99 ASN4 g 124 GLN4 g 193 GLN4 g 242 GLN3 h 120 GLN3 h 356 HIS4 i 110 ASN4 i 208 ASN4 i 238 ASN4 j 193 GLN5 k 157 ASN5 k 483 HIS5 k 506 GLN5 k 586 HIS

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Mol Chain Res Type6 m 15 HIS

5.3.3 RNA iO

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

5.5 Carbohydrates iO

There are no monosaccharides in this entry.

5.6 Ligand geometry iO

There are no ligands in this entry.

5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

There are no chain breaks in this entry.

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6 Map visualisation iO

This section contains visualisations of the EMDB entry EMD-7472. These are intended to permitvisual inspection of the internal detail of the map and identi�cation of artifacts.

6.1 Orthogonal projections iO

X Y Z

The images above show the map projected in three orthogonal projections, in greyscale.

6.2 Central slices iO

X Y Z

The images above show central slices of the map in three orthogonal directions, in greyscale.

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6.3 Largest variance slices iO

X Index: 875 Y Index: 753 Z Index: 612

The images above show the highest variance slices of the map in three orthogonal directions, ingreyscale.

6.4 Orthogonal surface views iO

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 2.5.This in conjunction with the slice images can indicate whether an appropriate contour level hasbeen selected.

6.5 Mask visualisation iO

This section was not generated. No masks were provided.

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7 Map analysis iO

This section contains the results of statistical analysis of the map.

7.1 Map-value distribution iO

The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.

Page 58 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

7.2 Volume estimate iO

The volume at the recommended contour level is 60862 nm3; this corresponds to an approximatemass of 54978 kDa.

The volume estimate graph shows how the enclosed volume varies with the contour level. Therecommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.

Page 59 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

7.3 Rotationally averaged power spectrum iO

Page 60 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

8 Fourier-Shell correlation iO

This section was not generated. No FSC curve or half maps provided.

Page 61 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

9 Map-model �t iO

This section contains information regarding the �t between EMDB map EMD-7472 and PDBmodel 6CGR. Per-residue inclusion information can be found in section 3 on page 8.

9.1 Map-model overlay iO

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 2.5 at50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of �t between the atomic model andthe map.

Page 62 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR

9.2 Atom inclusion iO

At the recommended contour level, 74% of all backbone atoms, 57% of all non-hydrogen atoms,are inside the map.