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

2. 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)

3. 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.

4. 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

5. 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 www.rcsb.org info@rcsb.org

6. 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

7. -snip- Header Origin Coordinates

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

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

11. Navigation Options

12. Query: The Top Search Box Autocomplete options

13. Advanced Search

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

15. Query Result Browser Overview Refinement options

16. Structure matches

19. Tabular Reports

20. Citation matches

21. Ligand hits

22. Exploring a Specific PDB ID: 1hho

23. Exploring 1hho – contd.

25. Context-sensitive 3D Viewers –Asymmetric unit –Biological assembly Biological assembly displayed by default Visualization Options For X-ray structures: presumed oligomeric state displayed

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

27. Exploring Ligand Environment

28. 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

29. 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

30. Resources/Tutorials Collection of tutorials: http://www.rcsb.org/pdb/static.do?p=education_disc ussion/educational_resources/index.html#tutorials http://www.rcsb.org/pdb/static.do?p=education_disc ussion/educational_resources/index.html#tutorials Getting started: http://www.rcsb.org/pdb/static.do?p=general_inform ation/getting_started/index.html http://www.rcsb.org/pdb/static.do?p=general_inform ation/getting_started/index.html Screencasts: http://www.rcsb.org/pdb/static.do?p=general_inform ation/screencasts.jsp http://www.rcsb.org/pdb/static.do?p=general_inform ation/screencasts.jsp Openhelix tutorial: http://www.openhelix.com/pdbhttp://www.openhelix.com/pdb Help: http://www.rcsb.org/pdb/staticHelp.do?p=help/index. html http://www.rcsb.org/pdb/staticHelp.do?p=help/index. html