1. Introduction to RCSB PDB Data, Tools and Resources
Maria Dominguez,
Shuchismita Dutta, Ph.D.

2. Learning Objectives
Introduction to PDB
RCSB PDB Query
Explore and Learn
Visualize and Analyze

3. Protein Data Bank (PDB)
First open access digital resource in biology (est with 7 entries)
Single global archive of 3-D macromolecular structures (contains >122,000 entries)
US PDB = RCSB PDB
Headquartered at Rutgers/UCSD (NSF, NIH, DOE)
Part of Worldwide PDB (with EU and Japan)
Makes PDB data freely available to all via
Some of the first few structures in the PDB

4. Why Use PDB Data? Visualize Analyze Compare Structures
The molecule, its parts or complexes
Analyze
Stability and interactions of the molecule
Structure function relationships
Compare Structures
Under different conditions
Bound to various molecules (ligands or partner proteins)
In health and disease
Engineer and Design
Mutations, additions, deletions to manipulate the function
Facilitate tracking
Discover drugs
2hhb/1hho

5. Where Does the Data Come From?
Sample  Structural Data Pipeline
Target
Selection
Isolation,
Expression,
Purification,
Crystallization
Data
Collection
Structure
Determination
PDB Deposition
& Release
X-ray
NMR
Structures in the PDB are experimentally determined – by X-ray crystallography, Nuclear Magnetic Resonance (NMR) or electron microscopy (EM).
In order to determine the structures a target is decided on, adequate amount of protein is produces and purified. For X-ray structures the protein has to be crystallized, for NMR a concentrated solution needs to be prepared, while for the EM experiment, the sample is placed on a grid. Data is collected in the respective experiments and used to build a model of the protein(s) in the structure. The structural coordinates and experimental data used to compute the models are all submitted to the PDB along with details about the experiment. The RCSB PDB enables users to freely access and use this material.
3D Models
Annotations
Publications EM
You come here  

6. PDB Data Atomic coordinates and primary experimental data
Experimental details - 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 sequence, function and other properties of the molecule.
Classification of structures by sequence, structure, function and other criteria
A Million files like this 
are downloaded every day
The primary data archived in the PDB are the 3D coordinates of all atoms in the structure. In addition information about the experiment, experimental data used to determine the structure and links to various other bioinformatics databases are also included.

7. Using the RCSB PDB Website …
Default View
View for Students and Educators
What can you do at the RCSB PDB website?
Query: find relevant structure(s)
Structure Summary: what is in the structure
Visualize: what does the structure look like
Integrate: to explore structure function relationships

8. Educational Resources (pdb101.rcsb.org)
Resources to help understand biology at molecular and atomic levels
Paper Models
Animations
Posters

9. Learning Objectives Introduction to PDB RCSB PDB Query
Search
Browse
Explore and Learn
Visualize and Analyze

10. Search and Refine By … Name, PDB ID, keywords
Entry properties e.g. author, deposition/release date, citation
Sequence
Annotations
Chemical components (ligands, drugs, etc.)

11. RCSB PDB Query Reports

12. Browse By Annotation For example Gene Ontology Source Organism
Biological process
Cellular component
Molecular function
Source Organism
Molecular Structure
SCOP
CATH
EC numbers
Membrane proteins
Anatomical Therapeutic Chemical

13. Search by PDB ID
PDB ID: A 4-character identifier for an entry in the Protein Data Bank, it is both unique and immutable. PDB IDs are the most direct method for retrieving structures from the database, these IDs are randomly assigned at the time of deposition and have no particular meaning. One or more PDB IDs can be typed or copied into the search box. Multiple ID searches can be done by separating these with commas or line breaks.

14. Learning Objectives Introduction to PDB RCSB PDB Query
Explore and Learn
Structure Summary Page
Links to Other Resources
Visualize and Analyze

15. Result: Search by PDB ID (4INS)
Seen on all pages - for new search from anywhere
Searching for a PDB entry by PDB ID will show this page – called Structure Summary Page
Entry specific information, details

16. Tabs on Top of Page Structure Summary 3D View Annotations Sequence
Overall structure information + details about composition of PDB structure
3D View
Options to interactively explore the structure
Annotations
Information about PDB structure or its components from other bioinformatics resource
Sequence
Of all polymers (protein, DNA, RNA) in the structure with annotations of secondary structure, mutations, etc.
Sequence Similarity
Comparison of given structure to entire PDB by sequence
Structure Similarity
Comparison of given structure to entire PDB by structure
Experiment
Details of how the structure of the Protein/Complex was determined
Literature
List of primary or other articles that reference the given structure
Not discussed here

17. Structure Summary Page -1
PDB ID
Display/Download file
Structure/Experiment Description; Validation Summary
Visualization of Structure
Literature
The literature box was introduced on the RCSB PDB website in With many publications made freely available online, the RCSB PDB took the opportunity to directly link structural data with the literature.

18. PDB Coordinates
The PDB archives 3D coordinates of molecular structures
By clicking on PDB Format, you can acquire the molecule’s 3D coordinates
The coordinates include residue name, residue #, X, Y, and Z coordinates for atoms, occupancy values, and B-factors.
Occupancy numbers are usually 1 (indicating that it is present at that location) or 0 indicating that it is not present at that location). It can sometimes have two or more different values for the same atom(s) (indicating that the atom may have alternate positions, due to conformational flexibility of the molecule). When there are multiple conformations it may be written as 0.5/0.5 (50:50), if two conformations are equally occupied, or any other ratios if they exist in disproportion.
B-factor refers to a temperature-dependent atomic vibrations as measured during the time of x-ray crystallography. Lower values of it indicate that the atom may be reliably located at that position.

19. Experiment Description
Angstrom is a unit of length, used to measure distances between atoms. 1Å = 10−10m (one ten-billionth of a meter)= 0.1 nm. An structure resolved at 1.5Å resolution is therefore of exceptional quality.
Like other HORMONES, Insulin circulates in the blood and regulates glucose uptake by cells/tissues.
The Insulin used for this experiment was derived from the organism Sus scrofa (or pig)
The description box presents a simple yet highly valuable overview of the molecule being analyzed.
Experimental Data and Validation: (refer to RCSB PDB website for further details:
Validation allows users to determine structure quality – does the structure model match the experimental data; does it agree with prior knowledge about its structure and function
The deposition authors are those responsible for solving this particular structure.
The structure was determined using X-Ray Diffraction.

20. Structure Summary Page - 2
Macromolecule Entities
Small Molecules
The blue bars in the Macromolecules box indicates the sequence of molecules in the PDB entry, matched against the UniProt sequence and various other domain and other annotations.
Small Molecules of Ligands are small molecules that may interact covalently or non-covalently to the proteins and DNA/RNA in the structure. Ligands have at least one atom and may have many atoms and complex connectivity and structure. Where available the ligand’s binding properties (when in complex with the protein/DNA/RNA) is also reported. This data is usually experimentally determined and derived from other bioinformatics data resources.

21. Macromolecular Entities
Indicates number of copies of this protein, and their polymer chain identifiers (chain ID)
This row indicates secondary structure. Yellow areas represent β-strands and red areas stand for α- helixes. See the exact residues involved in the helix/strand etc. using mouse-over options.
For each kind of protein (with a different polymer sequence) you can see the mapping of the region in the structure to the sequence of the complete gene product as listed in UniProt. Other annotations such as regions of helix and strands etc. are also marked here.
The results of clicking on the + sign in the left bottom corner of the box is shown in the next slide.
Clicking on this + sign will open the Protein Feature view (see next slide) displaying the region of the protein present in the structure, compared to the complete gene product.
Two copies of Insulin protein Chain B
Two copies of Insulin protein Chain A

22. PDB IDs and regions of protein included in the experiment
Protein Feature View
Links to UniProt with sequence, function and integration of links to various other bioinformatics resources
UniProt , Pfam, etc. annotations
This page maps all PDB entries that match the protein sequence listed under the UniProt ID. For example in this case the UniProt ID is P01315 (pig insulin). The lower panels list the PDB IDs and the regions (domains) that they map to on the UniProt (protein) sequence.
PDB IDs and regions of protein included in the experiment
Can use this page to identify other relevant structures – e.g. with different domains, mutations etc.

23. Structure Summary Page - 3
Experimental Data and Validation
Entry History
The blue bars in the Macromolecules box indicates the sequence of molecules in the PDB entry, matched against the UniProt sequence and various other domain and other annotations.

24. Learning Objectives Introduction to PDB RCSB PDB Query
Explore and Learn
Visualize and Analyze
3D Structures
Ligands and their neighborhood
Analyzing interactions

25. Visualization Metaphors/Conventions
What does a molecule look like?
Wireframe
Ribbons
Before delving into visualization it may be helpful to understand some basics about visualization. Here the coordinated may be represented as atoms and bonds, ribbons, or surfaces. Combinations of these representations may also be used
All atoms
Backbone
Spacefill

26. Visualize: Biological Assembly
Deposited coordinates (or Asymmetric Unit)
Toggle through various biological assemblies (monomer, dimer, trimer and hexamer)
Learn more about Biological Assemblies at

27. Visualize from Structure Summary Page
By clicking on the NGL, JSmol, or PV links you will be redirected to the 3D View Tab where you can explore the molecule’s visual further. These visualization tools can also be accessed from the 3D View tab and then by selecting the specific tool using the drop down menu options next to the image.
See next slide

28. 3D View (Jmol/JSmol) Display symmetry/ assembly
The Jsmol or Jmol tool is most popular online visualization software that can be directly used without installing any visualization software package
Structure display options
Explore interactions

29. Explore Ligand Interactions
Small molecular ligands, (ions, cofactors, inhibitors or drugs) found in a structure are usually important for its structure and/or function.
Exploring the interactions around ligands can highlight amino acid residues critical to the protein’s functions.
Exploring the kinds of interactions (hydrogen bond, hydrophobic, charge based etc.) can help understand the protein’s mechanism of action
Analyze interactions around ligand
Using online resources the environment of key ligands can be explored as shown above. The coordinates may also be visualized using other software e.g. Chimera, Pymol, etc. for analysis and making publication quality images.

30. Summary Introduction to PDB RCSB PDB Query Explore and Learn
Search
Browse
Explore and Learn
Structure Summary Page
Links to Other Resources
Visualize and Analyze
3D Structures
Ligands and their neighborhood
Analyzing interactions