Protein Data Bank: An Introduction Learning to Use the RCSB PDB Portal.

Protein Data Bank: An Introduction

Learning to Use the RCSB PDB Portal

What is the PDB?• Single international archive for 3D structural data

about biological macromolecules

• Used by scientists, educators, students, and general public

All PDB entries have unique alphanumeric IDs (e.g. PDB ID 1ABC)

Why care about protein structures?

•Visualize the molecule (or parts of it)•Clues to function•Compare and analyze structure•Understand normal functioning and disease states •Design/develop new medicine(diagnostic procedures, treatment)

– e.g. for diseases like avian flu, HIV, West Nile Virus, parts of the protein associated with Alzheimer’s disease, Cancers etc.

History of PDB1970s• Community discussions about protein structure archive• Protein crystallography meeting in Cold Spring Harbor • PDB established at Brookhaven (Oct 1971; 7 structures)

1980s• Number of structures increases as technology improves• IUCr guidelines established (PDB depositions increase)

1990s• Structural genomics begins• PDB moves to RCSB

2000s• wwPDB formed•RCSB PDB management renewal

2010s• PDB continues to grow

Number of released entries

Year

Where does the Data come from?

GenomicBased Target

Selection

DataCollection

StructureDetermination

Isolation, Expression,Purification,

Crystallization

PDB Deposition & Release

3D ModelsAnnotationsPublications

X-ray

NMR

EM

You come herewww.rcsb.org [email protected]

What is in the PDB?• Coordinate and experimental data files • Details about sample preparation, data collection and

structure solution• Sequence(s) of polymers (proteins and nucleic acids) in

the structure• Information about ligands in the structure

• Links to various resources that describe the sequence, function and other properties of the molecule.

• Classification of structures by sequence, structure, function and other criteria

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nloa

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lyLi

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d si

mila

r

Coordinate dataCoordinate data

Met

a da

taM

eta

data

-snip-

Header

Origin

Coordinates

Using the RCSB PDB Website

• Search – By name, sequence, ligands, author

• Browse

• Tabulate and create reports

• Download

• Visualize and Analyze

• Compare

RCSB PDB portal (www.pdb.org)Default View Student and Educator View

Student and Educator View

Navigation Options

Query: The Top Search Box

Autocomplete options

Advanced Search

Browse byBiological process, Cell Component, Molecular Function, E.C. numbers, Transporter classification, Source organism, Genome Location, MeSH, SCOP, CATH

Query Result BrowserOverview

Refinement options

Structure matches

Tabular Reports

Citation matches

Ligand hits

Exploring a Specific PDB ID: 1hho

Exploring 1hho – contd.

• Context-sensitive 3D Viewers– Asymmetric unit– Biological

assembly

• Biological assembly displayed by default

Visualization Options

• For X-ray structures: presumed oligomeric state displayed

Interactive 3D views of chain (Domain and Secondary structure) annotations

Exploring Ligand Environment

RCSB PDB Portal: Features/Functions• Your Question

– Search for entry (by ID, molecule name, author, sequence, ligand and PDB text etc.)

– Browse (by source organism, structure classification, biological process, function etc.)

• RCSB PDB’s Answer– Identify details of a structure, structure determination– Download data files for analysis and use – Create reports (tabular, drill down, collage)– Link to various other resources (e.g. PubMed, UniProt, SCOP,

CATH, GO etc.)– Links to Literature (primary citation and others that discuss

the structure)• RCSB PDB as a Resource

– Visualize structures, ligands, ligand interactions– Compare by sequence or by 3-D structure

MyPDB• Keep up-to-date with

new structures• Framework to store

user preferences• Saves queries in a

private account• Notifies users via email

when new structures match stored queries

Resources/Tutorials• Collection of tutorials:

http://www.rcsb.org/pdb/static.do?p=education_discussion/educational_resources/index.html#tutorials

• Getting started: http://www.rcsb.org/pdb/static.do?p=general_information/getting_started/index.html

• Screencasts: http://www.rcsb.org/pdb/static.do?p=general_information/screencasts.jsp

• Openhelix tutorial: http://www.openhelix.com/pdb• Help:

http://www.rcsb.org/pdb/staticHelp.do?p=help/index.html

Protein Data Bank: An Introduction Learning to Use the RCSB PDB Portal.

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