WWW.RCSB.ORG/PDB

Protein Data Bank(PDB)

CONTENTS

• Introduction• Supported and funded by• History• PDB Holdings list• Member organizations• Task forces• PDB ID• PDB File format• Browse to WWW.RCSB.ORG/PDB/

“The repository reservoir data bank to store the authenticated structures of Protein and Nucleic acid”

Single worldwide database and hundreds of secondary databases categorize the data differently.

Key resource in the area of structural biology, stores 3D structural data of large biological molecules such as Proteins and Nucleic acids.

Data is submitted by Biologists and Biochemists from all around the world to be freely accessible on internet via its member organizations’ websites and is updated weekly.

The mission is to maintain a single Protein Data Bank Archive of Macromolecular Structural data.

PROTEIN DATA BANKPDB

The Protein Data Bank (PDB) is operated by:

Rutgers, The State University of New Jersey.

The San Diego Supercomputer Center at the University of California, San Diego.

RCSB-the Research Collaborator for Structural Bioinformatics

The PDB is supported by funds from the National Science Foundation, the Department of Energy, and the National Institutes of Health.

SUPPORTED AND FUNDED

Two forces to initiate PDB:

Growing collection of sets of protein structural data by X-Ray diffraction.

NMR-nuclear Magnetic Resonance method to visualize protein structures in 3D, emerged in 1968.

In 1969, Dr Edger Meyer began to write software to store atomic coordinates files in a common format to make them available for geometric and graphical evaluation.

In 1971, one of Dr Meyer’s programs- SEARCH- enabled networking i.e enabled the researchers to access information from database to study protein structures offline.

PDB HISTORY

In 1973, upon Hamilton’s death, Dr Tom Koetzle took over direction of PDB for 20 years.

mmCIF project completed and Structural genomics began in 1970s.

In 1980s, IUCr guidelines established, number of structures deposited increases and independent biological databases established – e.g., the NDB.

In Oct, 1998; PDB was transferred to Research Collaboratory for Structural Bioinformatics (RCSB), complete transfer since 1999. Dr Helen M Berman of Rutgers University was the new director.

In 2003, with the formation of wwPDB, the PDB became an international organization having three member organizations.

In 2006, the BMRB joined PDB.

ExperimentalMethod

Proteins Nucleic AcidsProtein/Nucleic Acid

complexesOther Total

X-ray diffraction 62750 1323 3050 2 67125

NMR 7962 960 179 7 9108

Electron microscopy 262 22 96 0 380

Hybrid 41 3 1 1 46

Other 133 4 5 13 155

Total: 71148 2312 3331 23 76814

PDB HOLDINGS LIST ( as of 25 Oct, 2011)

Act as Data deposition, Data processing and Distribution centers for PDB data.

Three are founding member organizations:

PDBe…Protein Data Bank in Europe. PDBj…Protein Data Bank in Japan. RCSB…Research Collaboratory for Structural Bioinformatics.

The Biological Magnetic Resonance Data Bank (BMRB) joined later in 2006.

Another organization Worldwide Protein Data Bank (wwPDB) oversees PDB. wwPDB reviews and annotates each submitted entry and then it is automatically checked for plausibility( the source code) for validation software is available.

MEMBER ORGANIZATIONS

WW

PDB

X-Ray diffraction :-Spacing of atoms determined by location intensities spot on photographic plate by X-Ray e.g lyzozyme.

Limited to just crystal structures only

NMR (about 15% e.g., hemoglobin)…estimations of distances between pairs of atoms of proteins. Final conformation is obtained after solving distance geometry problem.

Illuminate dynamic side,conformatonal changes, protein folding as well

TASK FORCES

Each structure published in PDB receives a four character alphanumeric identifier or accession number. Like, 1ANG or 4hhb.

However, this cant be used as an identifier for biomolecules. Because several structures for the same molecule in different environments or conformations-are contained in PDB with different PDB IDs.

PDB IDENTIFIER (PDB ID)

HAEMOGLOBIN(2DN2)

Standard data representation…encoded in data dictionary. The metadata model supporting this representation is used by all PDB data processing and database software tools.

1. PDB file format was restricted to 80 characters per line initially.

2. In 1996, macromolecular Crystallographic Information File (mmCIF) format started.

3. In 2005, XML version called as PDBML, was described.

PDB FILE FORMAT

The Protein Data Bank (pdb) file format is a textual file format

describing the three dimensional structures of molecules held in the Protein Data Bank.

provides description and annotation structure atomic coordinates, side chains, secondary structure, as well as atomic connectivity

Water , ions, nucleic acids, ligands…

PDB file format

mmCIF is the acronym for the macromolecular Crystallographic Information File.

mmCIF is based on a subset of the syntax rules for the Self Defining Text Archive (STAR) file.

A Dictionary Description Language (DDL) defines the structure of mmCIF dictionaries. Dictionaries provide the metadata which define the content of mmCIF data files.

mmCIF data files, dictionaries and DDLs are all expressed in a common syntax.

mmCIF

basic information, more detailed

description of PDB, PDBML and mmCIF file formats

can be found at Protein Data Bank web sites.highly recommended to get familiar with all

rules of PDB format (such as gaps between columns)

BEACAUSE…

PDBML

put either a search term (for example, a protein name) or a PDB number

Point your browser to: www.rcsb.org/pdb/

RCSB PDB.htm

2DN2

RCSB PDB - 2DN2 Structure Summary.htm

UMINHAEMOGLOBIN

RCSB PDB - Query Results_HAEMOGLOBIN.htm

RCSB PDB - Query Results_homosepiense.htm

RCSB PDB - 2DN2 Structure Summary.htm

CLICK

If the contents of the PDB are thought of as primary data,

THENhundreds of derived (i.e., secondary)

databases categorize the data differently. For exampleSCOP & CATH :

categorize structures according to type of structure and assumed evolutionary relations;

 GO categorize structures based on genes.

Protein Annotation

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The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences

Class:the overall secondary-structure content of the domainArchitecture:high structural similarity but no evidence of homology.Topology:a large-scale grouping of topologies which share particular structural featuresHomologous superfamily:indicative of a demonstrable evolutionary relationship.

Pfam is a database of protein families that includes their annotations and multiple sequence alignment generated using hidden Markov models

CLICK

Select your desire method

CLICK

RCSB PDB - 2DN2 Literature Report.htm

CLICK

RCSB PDB - 2DN2 Biology and Chemistry Report.htm

CLICK

CLICK

RCSB PDB - 2DN2 Geometry Report.htm

& FINALLY

Structural View of BiologyShow the gradual updating released entries

You can also select different display view

can also download in different view

Text file can be viewed or modified in editor. Structure files may be viewed using various free and commercial

visualizations programs and Web browsers plug-ins like OPEN SOURCE PDB SOFTWERES Jmol Molekel MeshLab (able to import PDB data set and buildup surfaces

from them) QuteMol Avogadro OPEN BUT NOT FREE PYMOL , RASMOL, VIST PROT 3DS & STAR BIOCHEM

Viewing the data

http://www.rcsb.org/pdb/static.do?p=software/software_links/molecular_graphics.html

 The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plug-in.

RCSB PDB_softwere.htm

haemoglobin.pdb

central archive of experimentally solved bimolecular structures. But

only allows data retrieval does not provide collaboration or user feedback.

In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB.

provides tools for discussing and annotating proteins in a collaborative way.

Limitation

The Protein Data Bank (PDB) is the central archive of experimentally solved bimolecular structures. However, the PDB only allows data retrieval and does not provide functionality for collaboration or user feedback.

In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB. It provides tools for discussing and annotating proteins in a collaborative way. The goal is to create a central and freely-accessible repository of user-contributed information that will be useful for anyone working with PDB structures. As such PDBWiki can be considered a part of a wider effort in community-based biological databases curation.

Limitation

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