em maps and models in emdb/pdb. growth of em entries 680 286

EM Maps and Models in EMDB/PDB

Growth of EM entriesGrowth of EM entries

680

286

How EM experiments are archivedHow EM experiments are archived(~800 archived experiments as of Dec. 2009)

564

158

74*

*~1/3rd of PDB-only entries have deposited Structure Factors

Nuclear porecomplex, 85 ÅEMD-1097

Rotavirus V6protein, 3.8 ÅEMD-1461

Created by EBI in 2002 for archiving EM maps US deposition/annotation site added in 2008

680 released map entries

EM DataBankEM DataBank

Content of EMDB entries

EM map (ccp4 format) Experimental details (xml)

– sample information– specimen preparation– imaging parameters– reconstruction details– fitting details

Rarely: FSC resolution curves, images, layer lines or structure factors, map slices, masks

Validation of EMDB entries: What is checked? Metadata checked for consistency EMDB map:

– tested for valid CCP4 format – visually compared to original uploaded map– Map scale, map origin, author-recommended

contour level, map statistical profile, hand

80S ribosome

1s1h + 1s1i

EMD-1067

286 released entries

EM entries in the PDBEM entries in the PDB

T4 virus baseplate

1pdf+1pdi+1pdj+1pdl+1pdm+1pdp_2fl8+3h3w

EMD-1048

Content of PDB entries for EM structures

Atomic coordinate models fitted to EM maps Matrix representations and parameters for point

and helical symmetries Structure factors (2D crystals + some others) Experimental details

– sample information– specimen preparation– imaging parameters– reconstruction details– fitting details

Validation of EM entries in PDB: what is checked? Chemistry of the polymers Geometrical checks for inter and intra

molecular features Biological assembly

Issues

Sequence of model may not be sequence of sample

Geometry checks may fail because of modeling procedures used at resolution of experiment

Number of atoms and chains larger than can be accommodated in current PDB format

Not all models have deposited maps or structure factors

EM Deposition and Retrieval (2008)EM Deposition and Retrieval (2008)

Separate deposition and retrieval tools for maps and models

Impossible to cross-validate

EM Deposition and Retrieval TodayEM Deposition and Retrieval Today

Joint map+model deposition at two sites Maps and models are inspected together in

common annotation process

Common data model Data harvesting tools “One-stop shop” for deposition and retrieval Tools for visualization, segmentation, and

assessment

EM Deposition and Retrieval 2011EM Deposition and Retrieval 2011

Common Tool Project

wwPDB is creating a single interface for the deposition and processing of all structural biology data

EM will be part of the wwPDB

NIH GM079429 (Baylor, Rutgers, EBI) 2007- 2012UK BBSRC BBG0225771 (EBI) 2009-2012

Project Team

Wah ChiuMatthew BakerSteven LudtkeIan ReesJoe Warren (Rice U)Powei Feng (Rice U)

Helen BermanCatherine LawsonBatsal DevkotaRaship ShahRaul SalaJohn Westbrook

Gerard KleywegtChristoph BestGlen van GinkelSameer Velankar

Kim Henrick Richard Newman

Open Questions

What other data should be collected? Are there data that should not be collected? How should the maps be validated? How should the models be validated? Who should make the recommendations?