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2 Introduction To PDB

The document discusses the Protein Data Bank (PDB), which is a central archive of experimentally determined macromolecular structures. It provides key information like protein structures, functions, and interactions. The PDB started in 1971 with 7 structures and has now grown significantly. It is jointly managed by four organizations as part of the worldwide Protein Data Bank to ensure open access and long-term preservation of the structural data.

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Rigel_T
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
34 views

2 Introduction To PDB

The document discusses the Protein Data Bank (PDB), which is a central archive of experimentally determined macromolecular structures. It provides key information like protein structures, functions, and interactions. The PDB started in 1971 with 7 structures and has now grown significantly. It is jointly managed by four organizations as part of the worldwide Protein Data Bank to ensure open access and long-term preservation of the structural data.

Uploaded by

Rigel_T
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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An introduction to the

Protein Data Bank

Gary Battle
Protein Data Bank in Europe
What to expect

What can we learn from structures?


Why centrally archive data?
The PDB archive and wwPDB
PDBe at EMBL-EBI
What can we learn
from structures?

It has not escaped our


notice
Possible answers
Clues about function, mechanism, Conformational changes (if >1 structure)
specificity,
Evolutionary relationships
Active/catalytic site(s) Dynamics
Distribution of residues (charged,
hydrophobic)
Surface properties
Secondary structure Flexibility
Domain organisation Cavities, channels,
Evolutionary relationships
Disulfide links, H-bonds,
Effect of mutations
Similarity to other proteins
Ligand(s) + interactions
Shape, size
Fold Potential interaction sites
Structural motifs Cellular location
Oligomeric state
Distances, angles, ...
Transmembrane regions
Co-factors, metal ions, ligands,
Glycosylation state
Interaction surfaces
Clues about function from structure
Why do we need a central
structure archive?
Why is it useful to collect, store and disseminate
data using a centralised repository?
Accessibility
Persistence
Context
Further analysis
Accessibility
One-stop shop
Uniform data representation/annotation

Persistence
Typical websites have a half-life of 2 years
Professional management

Context
Comparisons against all other entries
Validation
Integration with other resources

Facilitate further analysis


Database-wide studies and data-mining
PDB

The single global repository for


experimentally determined
macromolecular structures - the
Protein Data Bank (PDB)
Established 1971
Walter Hamilton @ Brookhaven
7 Structures
PDB format
Magnetic tape distribution
Petition for a central
repository for atomic
coordinate data of
protein structures

American Crystallographic
Association Winter
Meeting, Columbia, SC,
Feb. 1971
Announcing the
Protein Data Bank

Nature New Biology


Vol. 233 October 20 1971
The Protein Data Bank in 1973
Growth of the PDB
wwPDB

Mission: to maintain a
single PDB archive of
macromolecular structural
data that is freely and
publicly available to the
global community.
Celebrated 10 year
anniversary in 2013
A truly global resource
More than 400 million structure downloads in 2013
Value of the PDB
The archive cost is ~1% of the
cost of generating the data
Value of archive currently ~9 billion US$
Annual research cost ~1 billion US$
Global annual cost of wwPDB ~10 million US$

Immeasurable scientific value


Value of the PDB
Electron Microscopy Data Bank (EMDB)
Global public repository for EM density maps of macromolecular complexes
and subcellular structures
Founded at EBI in 2002
Jointly operated by PDBe, RCSB and NCMI
PDBe EM portal provides advanced search, visualisation and analysis
services. http://pdbe.org/emdb
Growth of EMDB

pdbe.org/emstats
Image gallery of EM structures in EMDB and PDB

Lawson C L et al. Nucl. Acids Res. 2011;39:D456-D464


PDBe at EBI

Deposition and annotation site for structural data on


biomacromolecules (X-ray, NMR, EM)
Mission: Bringing structure to biology
Integration: turn PDB into an invaluable integrated resource
for the entire biomedical community
Validation: assessing and improving structure quality
Advanced services: develop high-quality value-added
content and services
Data resources at EMBL-EBI Literature & ontology
Europe PubMed
Nucleotide sequences Central
Genomes & variation
European Nucleotide Gene Ontology
Ensembl
Archive (ENA)
Ensembl Genomes
Genome-phenome archive
Metagenomics
Expression Molecular structures
Array Express Protein Data Bank in Europe
Expression Atlas PDBsum
PRIDE
Proteins R-Workbench
The Universal Protein
Resource (UniProt)
InterPro
Chemical biology
ChEMBL Systems
ChEBI
BioModels
Patent sequences
Enzyme Portal
Non-redundant patent
Pathways BioSamples
sequence dbs
IntAct
Patent compounds
Reactome
Metabolights
SIFTS - Structure integration with function,
taxonomy and sequence

pdbe.org/sifts
SIFTS
Authoritative source of up-to-date residue-level mappings
between PDB entries and other data resources
Updated with each weekly PDB release
Exported in XML format (separate file for each PDB entry)
and as tab-delimited file (entire archive)
Available from
PDBe website http://pdbe.org/sifts
EBI FTP site ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts

Velankar et al., Nucleic Acids Research, 41 (D1), D483-D489.


Reactome pathway browser

Reactomes pathway
browser allows
biologists to navigate
and visualize pathway
and network data
http://www.reactome.org/
Now offers easy access
to 3D structural data
and citations for
proteins that are
archived in the PDB.
To err is human
Experimental structures
May contain errors!
Need for validation
Botulin neurotoxin type b catalytic
domain with inhibitor bound
1FQH (2000, 2.8, JACS)

Bad geometry: residue TRP Crystal structure of inhibitor of


D67 in PDB entry 7GPB KappaB kinase Beta. Nature,
472, 325-330 (2011)
Not all protein models were created equal

Using a model that is


inappropriate to the
ligands you are docking
will lead to poor results
CCDC virtual screening
simulations using
different protein models
with the same ligand/
decoy sets
demonstrate this
Validation Reports
Generated and sent to
depositors during annotation
since Aug. 1, 2013
Standalone server for
assessing structures prior to
submission
Support depositors, journal
editors and referees
Validation reports available for
all X-ray structures
Help (non-expert) users
assess individual models
PDBeFold
Interactive comparison, alignment and superposition based
on protein secondary structure.

Find similar structures: pdbe.org/fold


PDBePISA
Exploration of macromolecular (protein, DNA/RNA and
ligand) interfaces and prediction of probable quaternary
structures.

Predict quaternary structure: pdbe.org/


pisa
PDBeMotif
Flexible 3D search and analysis of protein-ligand
interactions, binding environments and structural motifs.

Analyse binding sites and motifs: pdbe.org/


motif
NMR resources and services
Visualisation and validation of NMR models and data.

NMR resources:
pdbe.org/nmr
EM resources and services
Comprehensive search and analysis tools for EMDB entries.

EM resources:
pdbe.org/em
Cool stuff from PDBe
Latest PDB, EMDB, chemistry, biology

pdbe.org/latest
Educational resources: Quips
Interactive exploration of interesting structures from the PDB

Quite interesting PDB structures: pdbe.org/


quips
Widgets for your own web pages

UniPDB

PDBportfolio
PDBprints
Biobar

pdbe.org/biobar
Biobar
Challenges

Growth
Number, size, complexity of entries
Hybrid, low-resolution methods and models
From molecular to cellular structural biology
From structural biology archive to biomedical resource
Best-practice models versus published models
New ways of accessing and using structural information
PDBe collaborations & interactions
wwPDB EBI EMBL
RCSB UniProt Svergun & Gavin
PDBj ChEMBL Academic groups
VTFs
BMRB ChEBI
GENOME-3D
EMDB Thornton group
WeNMR
RCSB IntEnz OME
NCMI IntAct NORINE
CAPRI
CCDC Ensembl
SGC
CCPN Europe PMC
Vuister lab
CCP4 Pfam/InterPro Birkbeck
CCP-EM GOA Companies
INSTRUCT Reactome OpenEye
NextMove

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