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 PDB 1970s 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? Genomic Based Target Selection Data Collection Structure Determination Isolation, Expression, Purification, Crystallization PDB Deposition & Release 3D Models Annotations Publications X-ray NMR EM You come here

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 Download/Use directly Link to/Find similar Coordinate data Meta data

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Using the RCSB PDB Website Search –By name, sequence, ligands, author Browse Tabulate and create reports Download Visualize and Analyze Compare

RCSB PDB portal ( Default ViewStudent and Educator View

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Query: The Top Search Box Autocomplete options

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

Query Result Browser Overview Refinement options

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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 when new structures match stored queries

Resources/Tutorials Collection of tutorials: ussion/educational_resources/index.html#tutorials ussion/educational_resources/index.html#tutorials Getting started: ation/getting_started/index.html ation/getting_started/index.html Screencasts: ation/screencasts.jsp ation/screencasts.jsp Openhelix tutorial: Help: html html