EM Maps and Models in EMDB/PDB

Growth of EM entries

How EM experiments are archived (~800 archived experiments as of Dec. 2009) * *~1/3 rd of PDB-only entries have deposited Structure Factors

Nuclear pore complex, 85 Å EMD-1097 Rotavirus V6 protein, 3.8 Å EMD-1461  Created by EBI in 2002 for archiving EM maps  US deposition/annotation site added in released map entries EM 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 released entries EM 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)  Separate deposition and retrieval tools for maps and models  Impossible to cross-validate

EM 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 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 GM (Baylor, Rutgers, EBI) UK BBSRC BBG (EBI) Project Team Wah Chiu Matthew Baker Steven Ludtke Ian Rees Joe Warren (Rice U) Powei Feng (Rice U) Helen Berman Catherine Lawson Batsal Devkota Raship Shah Raul Sala John Westbrook Gerard Kleywegt Christoph Best Glen van Ginkel Sameer 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?