1. EM Maps and Models in EMDB/PDB

2. Growth of EM entries 680 286

3. How EM experiments are archived (~800 archived experiments as of Dec. 2009) 564 158 74* *~1/3 rd of PDB-only entries have deposited Structure Factors

4. 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 2008 680 released map entries EM DataBank

5. 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

6. 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

7. 80S ribosome 1s1h + 1s1i EMD-1067 286 released entries EM entries in the PDB T4 virus baseplate 1pdf+1pdi+1pdj+1pdl +1pdm+1pdp_2fl8+3h3w EMD-1048

8. 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

9. Validation of EM entries in PDB: what is checked?  Chemistry of the polymers  Geometrical checks for inter and intra molecular features  Biological assembly

10. 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

12. EM Deposition and Retrieval (2008)  Separate deposition and retrieval tools for maps and models  Impossible to cross-validate

13. EM Deposition and Retrieval Today  Joint map+model deposition at two sites  Maps and models are inspected together in common annotation process

14.  Common data model  Data harvesting tools  “One-stop shop” for deposition and retrieval  Tools for visualization, segmentation, and assessment EM Deposition and Retrieval 2011

15. 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

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

17. 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?