Post on 17-Jan-2016
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 info@rcsb.org
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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d/U
se d
irect
lyLi
nk to
/Fin
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
Structure matches
Structure matches
Tabular Reports
Citation matches
Ligand hits
Exploring a Specific PDB ID: 1hho
Exploring 1hho – contd.
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