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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 - PowerPoint PPT Presentation
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EM Maps and Models in EMDB/PDB
Growth of EM entriesGrowth of EM entries680
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?
