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