EMBL-EBI MSD database is structured around the fact that Proteins are “sticky”
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Transcript of EMBL-EBI MSD database is structured around the fact that Proteins are “sticky”
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EMBL-EBI
MSD database is structured around the fact that Proteins are “sticky”
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EMBL-EBI
A short biography of 1 protein whose very existence depends on being as sticky as possible
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EMBL-EBI
EMBL K02078
ttaacgcgta aattcaaaaa tctcaaattc cgacccaatc aacacacccg ataccccatg ccaataaaaa agtaacgaaa atcggcacta aaactgacaa ttttcgacac tgccgccccc ctacttccgc aaaccacacc cacctaaaag aaaatacaaa ataaaaacaa ttatatagag ataaacgcat aaaatttcac ctcaaaacat aaaatcggca cgaatcttgc tttataatac gcagttgtcg caacaaaaaa ccgatggtta aatacattgc atgatgccga tggcaagccc tgaggctttc ccctttcaat taggagtaat tttatgaata cccttcaaaa aggctttacc cttatcgagc tgatgattgt gatcgctatc gtcggcattt tggcggcagt cgcccttccc gcctaccaag actacaccgc ccgcgcgcaa gtttccgaag ccatcctttt ggccgaaggt caaaaatcag ccgtcaccga gtattacctg aatcacggca aatggccgga aaacaacact tctgccggcg tggcatcccc cccctccgac atcaaaggca aatatgttaa agaggttgaa gttaaaaacg gcgtcgttac cgccacaatg ctttcaagcg gcgtaaacaa tgaaatcaaa ggcaaaaaac tctccctgtg ggccaggcgt gaaaacggtt cggtaaaatg gttctgcgga cagccggtta cgcgcaccga cgacgacacc gttgccgacg ccaaagacgg caaagaaatc gacaccaagc acctgccgtc aacctgccgc gataaggcat ctgatgccaa atgaggcaaa ttaggcctta aattttaaat aaatcaagcg gtaagtgatt ttccacccgc ccggatcaac ccgggcggct tgtcttttaa gggtttgcaa ggcgggcggg gtcgtccgtt ccggtggaaa taatatatcg at
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EMBL-EBI
MNTLQKGFTL IELMIVIAIV GILAAVALPA YQDYTARAQV SEAILLAEGQ KSAVTEYYLN HGKWPENNTS AGVASPPSDI KGKYVKEVEV KNGVVTATML SSGVNNEIKG KKLSLWARRE NGSVKWFCGQ PVTRTDDDTV ADAKDGKEID TKHLPSTCRD NFDAK
UniProt P02974
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EMBL-EBI
PDB 1AY2
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MSD DATABASE
pentamer
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MSD DATABASE
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negatively stained TEM images
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Neisseria gonorrhoeae expressing pili and interacting with epithelial cells. The pili are polar flexible filaments of about 5.4 nm diameter and 2500 nm average length.
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Type IV Pilin Structure and Assembly: X-Ray and EM Analyses of Vibrio cholerae Toxin-Coregulated Pilus and Pseudomonas aeruginosa PAK Pilin
L. Craig, et al Molecular Cell, 11, 1139–1150, 2003
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EMBL-EBI
Type IV pili are not merely passive sticky fibres but dynamic machines that participate in a surprising number of functions including:
Bacterial aggregation Adhesion to host cells Twitching motilityPilus retraction DNA transformation In another bacterial species, motility. Phage receptor in V. cholerae.
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EMBL-EBI
EMBL
UniProt
PDB
Assembly (MSD)
Microscopy
still not the full story - GENOME
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EMBL-EBI
Pilus gene organisation
Many copies of pilin gene throughout chromosome
Two are functional, pilE1 and pilE2 All other copies are silent Antigenic variation occurs due to
recombination (within mini-cassettes)
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EMBL-EBI
Antigenic variation in N. gonorrhoeae
A single cell can give rise to daughter cells expressing structurally and antigenically different pili
Gonococcus has the genetic capacity to make as many as a million different pilin variants
All able to bind to same host tissues and to cause the same disease symptoms
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EMBL-EBI
PDB Entries and X-Ray results
1. Crystal Structure
2. Molecular Structure (covalent)
3. Oligomeric Assembly
What has all this got to do with MSD?
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EMBL-EBI
Chains Residues AtomsExp. Result Assembly
ALT
ASSEMBLY
ASSEMBLY DATA
ATOM
ATOM DATA
CHAIN
COMPONENT
DEPOSITION
MODEL
atd_component_fkatd_component_fk
assembly_deposition_fk
assembly_deposition_fk
assembly_a_data_fk
assembly_a_data_fk
assembly_data_model_fk
assembly_data_model_fk
atd_alt_fk
atd_alt_fk
atd_atom_fk
atd_atom_fk
atd_chain_fk
atd_chain_fk
chain_assembly_fk
chain_assembly_fk
atd_model_fk
atd_model_fk
MSD Relational Database
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EMBL-EBI
KEY to MSD DataBase
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EMBL-EBI
Biological Context
PDB MSD
Oxalate oxidase 1FI2 hexameric
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EMBL-EBI
PDB Xray coordinates
PDB entry the deposited coordinates usually consist of the contents of the asymmetric unit:
The contents of the ASU define a single copy of the macromolecule
The contents of the ASU consist of more than one copy of the macromolecule
The contents of the ASU require crystallographic symmetry operations to be applied to generate the complete macromolecule(s)
A combination of the above, including multiple copies and required symmetry transformations
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EMBL-EBI
benzene
C6H6
Covalent bonded
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EMBL-EBI
Benzene crystallised in
Space Group P6/m
6-fold rotation axis
Mirror plane
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EMBL-EBI
Benzene P6/m in the PDB
ATOM C1 x1 y1 z1 occupancy 0.5
ATOM H1 x2 y2 z2 occupancy 0.5
Entire atomic contents:
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EMBL-EBI
The stronger of the two is the hydrogen bond.
The weaker is the van der Waal's forces.
Both interactions depend on the same fundamental cause, the charge on electrons, and how that results in attraction and repulsion at an atomic level.
HELD TOGETHER BY WEAK FORCES
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EMBL-EBI
Quaternary Structure
Quaternary Structure is defined as that level of form in which units of tertiary structure aggregate to form homo- or hetero-multimers.
Consideration of the presence of a quaternary state is important in the understanding of a protein's biological function.
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Crystal Structure
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Crystal Structure
Oligomeric Assembly
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EMBL-EBIProteins don’t do this –
pack by translationals
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EMBL-EBI
There are three main types of symmetry:
symmetry with respect to a plane (mirrors) symmetry with respect to a line (rotations) symmetry with respect to a point (inversions)
Symmetry
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EMBL-EBI
symmetry with respect to a line (rotations)
symmetry with respect to a plane (mirrors) symmetry with respect to a point (inversions)
Symmetry
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EMBL-EBI
1, 2, 3, 4, 6 -fold rotational symmetry
These are the only rotational symmetries that can exist in crystals; all others are disallowed. These five rotational axes are called the five Proper Axes
Symmetries showing 5-, 7-, 8-, 9-, 10-, 11-, & 13- fold rotations are known for biological molecules – these are observed in the Asymmetric Unit.
Rotational symmetry
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1g8h
Applying 1st 3-fold Rotation
A
A’
Residues of Chain A in interface
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A
A’ Residues of Chain A’ in interface
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Applying 2nd 3-fold Rotation
A
A’
A”
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Also has a 2-fold rotation
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Final Assembly is a Hexamer from 23 symmetry
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EMBL-EBI
If you add translations to rotation axes, you form what are call screw axes. For an nm screw axis, the rotational component is 360/n degrees, and the translations is m/n of the unit translation along the axis.
In Biological Crystallography --> Polymers
Helices are improper Screw axes – e.g. DNA
Screw Axes
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EMBL-EBI
Also has a 2-fold rotation – infinite cylinder in crystal
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Screw Axis
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EMBL-EBI
Screw Axes example
tubulins
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EMBL-EBI
SYMMETRY Rules –BUT What about -
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What happened to symmetry?
2:1 hetero-complex
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The Ribosome – the champion Heterocomplex
proteins tossed around the RNA
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protein aggregates complicate the lives of people who study proteins in vitro
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Protein Aggregation and Amyloid Diseases- Converting the protein from a soluble to a fibrillar structure