CCP-EM community meeting7 February 2013
EMDB and beyond
Ardan Patwardhan and Gerard KleywegtProtein Data Bank in EuropeEMBL-EBI
Outline• Introduction • EMDB services• Community consultations• Plans
pdbe.org
ebi.ac.uk
GenomesEnsembl
Ensembl Genomes EGA
Nucleotide sequenceENA Functional genomics
ArrayExpress, Expression Atlas
Protein sequencesUniProt
Protein families + motifs InterPro, Pfam
Molecular &cellular structure
PDBeProtein expression
PRIDE
Chemical entitiesChEBI
Interactions + pathways
IntAct, Reactome
Literature and ontologiesCiteXplore, UKPMC, (GO)
ChemogenomicsChEMBL
SystemsBioModels
PDBe at a glance• Mission: Bringing Structure to Biology• Founding partner of Worldwide Protein Data Bank
(wwPDB)• Founder of Electron Microscopy Data Bank (EMDB)• Major activities:
• Deposition and annotation site for structural data on biomacromolecules (X-ray, NMR, EM)
• Integrated resource to serve structural data and information
• Liaise with structural biology community• Guided by advisory bodies
• PDBe, wwPDB, EMDataBankpdbe.org
Electron Microscopy Data Bank• Founded at EBI in 2002• Since 2007 - operated jointly by PDBe and RCSB
• NIH grant to NCMI + RCSB + PDBe (5 years)• RCSB as second deposition site• Integrate EMDB deposition with PDB (common tool)• Operate joint portal - EMDataBank.org• Policy harmonisation EMDB/PDB
• Additional funding from BBSRC and EMBL-EBI• Own advisory board and validation task force
• From 2013 - expecting renewal of NIH grant and supportfrom EMBL-EBI and EU (BioMedBridges)
EMDB holdings
pdbe.org/emstats
Single particle78%
Sub-tomogramaveraging
9%
Helical9%
Tomography3% Electron
crystallography1%
66 maps released in January!
EMDB services
Searching EMDB• Advanced search: pdbe.org/emsearch• Browse archive: pdbe.org/embrowse
pdbe.org/emdb
Visualisation• 3D viewer for all entries, e.g.
pdbe.org/emd-2238/volume• Slice viewer for tomograms, e.g. pdbe.org/emd-
1906/slice
Analysis pages• Map/model overlays• Map/mask overlays• Atom-inclusion plots• FSC curves
pdbe.org/emd-####/analysis
emd-2017, PDB: 4adv
Community consultations
EM Validation Task Force, 2010• Recommendations on map validation, model
validation and map/model validation• Henderson et al., Structure 20, 205 (2012)
DOI: 10.1016/j.str.2011.12.014
DMCEM, 2011• “Data-Management Challenges in
3D Electron Microscopy”• Recommendations:
• Work with tomography community to encourage deposition
• Set up a test-image repository• Develop and promote standardisation of file formats to
capture richer content• Promote and encourage good practices w.r.t validation
by providing web-based validation services• Patwardhan et al., Nature SMB 19, 1203 (2012)
DOI: 10.1038/nsmb.2426
3DEM GRC, 2012• Special discussion session on tomography deposition• Agreed on statement, circulated on 3DEM mailing list
• Subtomogram-averaged reconstructions mandatory deposition
• Tomographic reconstructions deposition of at least one representative tomogram strongly recommended
• Overall positive response
3DCC4MW, 2012• “3D Cellular Context for the Macromolecular World”• New exciting cellular imaging techniques such as
FIB/SEM and soft X-ray tomography• Added value for general biologists when different
scales of imaging/structure are linked together• PDBe encouraged to:
• Set up pilot archive for 3DSEM and SXT• Capture correlative LM in EMDB and pilot archives• Set up archiving facility for movies
• Meeting report to be published
Plans
New deposition and annotation system (D&A)• Joint wwPDB project – same system to be used by all
wwPDB partners• Consistent interface for the deposition of
EM/X-ray/NMR models and data:• Atomistic models, X-ray/NMR data PDB• EM/ET data, masks EMDB• (Additional NMR data BMRB)
• Better support for hybrid methods• Value-added validation to be integrated with the
system
EM validation services• Promote and encourage good practices and
consistency in reporting results• FSC server will request relevant meta-data/data,
calculate and display results, and create a file that can be uploaded into our deposition system
• Other ideas:• Tilt-pair validation server (from Peter Rosenthal’s lab)• Simulate SAXS profiles (and compare to actual data?)• Examine Euler-angle distribution/data completeness
Search service based on volume data• BioMedBridges project – collaboration with STFC
(Martyn Winn)• Search for matches in database of shapes derived
from PDB and EMDB• Automated segmentation and fitting as EMDB/PDB
grow• Check fits that are deposited• Align related structures
http://www.biomedbridges.eu/workpackages/wp9
Pilot test-image repository• Not very prescriptive to start with: micrographs,
picked particles, and tilt series• Minimal manual entry of meta-data
• Link entries with EMDB• Harvest info from EPU, EMX, etc.
• Use Aspera for data transfer, OMERO for data presentation
Pilot 3DSEM and SXT archive• Recommendation of 3DCC4MW meeting• Use technology already used for other archives• Data model needs to be adapted for 3DSEM and SXT• Will require new funding
Movie archive linked to EMDB and PDB• Develop using YouTube API• Movies stored on YouTube• Service to capture meta-data linking frames to
entries
What do we hope to get from CCP-EM?• Input on activities and plans• Identifying use-cases• Support in terms of data, and usage/testing of
services• Evaluation of software• APIs and libraries needed to work with data and
move it around
Questions & discussion
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