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EM Maps and Models in EMDB/PDB

EM Maps and Models in EMDB/PDB. Growth of EM entries. 680. 286. How EM experiments are archived. (~800 archived experiments as of Dec. 2009). 158. 74*. 564. *~1/3 rd of PDB-only entries have deposited Structure Factors. Created by EBI in 2002 for archiving EM maps

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EM Maps and Models in EMDB/PDB

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  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) 158 74* 564 *~1/3rd of PDB-only entries have deposited Structure Factors

  4. Created by EBI in 2002 for archiving EM maps US deposition/annotation site added in 2008 EM DataBank Nuclear pore complex, 85 Å EMD-1097 Rotavirus V6 protein, 3.8 Å EMD-1461 680 released map entries

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

  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

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

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

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

  14. 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

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

  16. 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?

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