Protein Data Bank
Radka Svobodová
CEITEC Masaryk University
Why archive research data?
• 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
Macromolecular structures (1950-1980)
• Myoglobin (1958) – Kendrew et.al. - The most striking
features of the molecule were its irregularity and its total
lack of symmetry
• Lysozyme (1965) – Phillips et.al.
• Ribonuclease (1967) – Kartha, Bello &Harker
• Papain (1968) – Drenth et.al.
• Haemoglobin (1968) – Perutz et.al. – Stereochemistry of
cooperative effects in Haemoglobin – M.F. Perutz (1971)
• Insulin (1971) – Blundell et.al.
• PDB was established in 1971 with 7 structures
• 1946 Sumner “Enzymes can be crystallised”
• 1962 Crick, Watson, Wilkins DNA
• 1962 Perutz & Kendrew Haemoglobin & myoglobin
• 1972 Anfinsen, Moore & Stein Ribonuclease
• 1982 Klug Nucleic acid-protein complexes (TMV)
• 1988 Deisenhofer, Huber & Michel Photosynthetic RC
Immeasurable scientific value
Many PDB-derived databases/resources!
• Since 2011, >25% of new databases described in annual
NAR Database issues used PDB data (119 of 452)
• In total, >200 databases (of 1685 in Jan-2016 NAR
Database collection) use PDB data, including:
• 123 structure databases
• 49 sequence databases
• 22 metabolic and signalling
pathways databases
Data (2016) from Monica Sekharan, RCSB-PDB
Cost of relocating the PDB archive
• Current PDB holdings exceed 123,456 experimentally
determined 3D structures of biological macromolecules
• Estimated cost of replicating a PDB entry ranges between
US$50,000 to US$250,000
• Conservative cost of replicating the PDB archive
(assuming average unit cost of US$100,000) equals
US$12 billion
6
Infected
Cell
Virus
Assembly Chains
Complex Molecule
• CLEM
• 3DSEM
• SXT
• X-ray
• NMR
• EM Atom
Chemical
Entity
Organism
• ET
• SAXS
• EM
Molecular and cellular structures
Not in the picture: Biological context, Time ….
PDB (1971)
EMDB (2002)
EMPIAR (2014)
EMDB –
Electron Microscopy
Data Bank
EMDB - Electron Microscopy Data Bank
• Archives 3DEM and electron
tomography volume data
• Founded at EMBL-EBI in
2002
• Operated jointly by PDBe and
RCSB since 2007 (PDBj
annotates since 2013)
• >4100 entries (Oct-16)
emdb-empiar.org emdatabank.org
EMDB holdings (Sep-2016)