CCP-EM community meeting 7 February 2013 EMDB and beyond Ardan Patwardhan and Gerard Kleywegt Protein Data Bank in Europe EMBL-EBI

Outline Introduction EMDB services Community consultations Plans pdbe.org

ebi.ac.uk Genomes Ensembl Ensembl Genomes EGA Genomes Ensembl Ensembl Genomes EGA Nucleotide sequence ENA Nucleotide sequence ENA Functional genomics ArrayExpress, Expression Atlas Functional genomics ArrayExpress, Expression Atlas Protein sequences UniProt Protein sequences UniProt Protein families + motifs InterPro, Pfam Molecular & cellular structure PDBe Molecular & cellular structure PDBe Protein expression PRIDE Protein expression PRIDE Chemical entities ChEBI Chemical entities ChEBI Interactions + pathways IntAct, Reactome Interactions + pathways IntAct, Reactome Literature and ontologies CiteXplore, UKPMC, (GO) Literature and ontologies CiteXplore, UKPMC, (GO) Chemogenomics ChEMBL Chemogenomics ChEMBL Systems BioModels Systems BioModels

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, EMDataBank pdbe.org

Electron Microscopy Data Bank Founded at EBI in 2002 Since 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 expecting renewal of NIH grant and support from EMBL-EBI and EU (BioMedBridges)

EMDB holdings pdbe.org/emstats Single particle 78% Sub-tomogram averaging 9% Helical 9% Tomography 3% Electron crystallography 1% 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: /j.str

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: /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

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