Summary of Joint European and United States 3D-EM Activities
The number of protein structure determinations using x-ray and NMR methods has grown over the last thirty years. In the past decade the growth of structures determined using cryo-Electron Microscopy (cryoEM) is steadily increasing and is expected to accelerate. Groups from Europe and the US have been actively collaborating on defining data dictionaries and standards for cryoEM structure deposition. This work builds on initial EU projects: the pilot project BioImage and the development EU Project IIMS (http://www.ebi.ac.uk/msd/projects/IIMS.html). The latter project established the first 3D Electron Microscopy deposition/archive system (EMDep; http://www.ebi.ac.uk/msd-srv/emdep/) and associated relational database (EMdb; http://www.ebi.ac.uk/msd-srv/emsearch) at the EBI, and XML data representation.
The data definition dictionaries also covered extensions for deposition of fitted coordinates to the Protein Data Bank (PDB); this is the result of an extensive collaboration between the EBI/IIMS partners and the RCSB, in particular with Monica Chagoyen (Madrid), Richard Newman (EBI) and John Westbrook (RCSB) (see http://mmcif.pdb.org/dictionaries/mmcif_iims.dic/Index/ and http://iims.ebi.ac.uk/3dem_pdb.html).
The IIMS project started a series of workshops with many participants from both Europe and the US (see for example http://www.ebi.ac.uk/msd/iims/report.html).
Support for EMdep has continued in Europe with the establishment of the PF6 Network of Excellence 3D- EM on New Electron Microscopy Approaches for Studying Protein Complexes and Cellular Supramolecular Architecture (http://www.3dem-noe.org/). This consortium has held several developer workshops, including one to set NoE standards for data exchange (3D-EM New Electron Microscopy Approaches for Studying Protein Complexes and Cellular Supramolecular Architecture Developers Workshop; May 27 - 28th 2004, hosted by the EBI at Jesus College, Cambridge; http://www.ebi.ac.uk/msd/workshops/3DEM/3DEM_1.html).
This collaboration has been extended with international workshops held in the US to further develop the data definitions required to enhance EMdep and EMdb, and to investigate how to improve the linking of PDB fitted coordinates from EM reconstructions with deposited maps. One workshop hosted by the RCSB was held at Rutgers (October 23-24, 2004; http://rcsb-cryo-em-development.rutgers.edu/workshop/). This workshop was co-sponsored by the Computational Center for Biomolecular Complexes (C2BC). The C2BC (http://ncmi.bcm.tmc.edu/ccbc) is supported by the Inter-disciplinary Research Roadmap Initiatives at National Institutes of Health intending to bring together scientists from different disciplines to develop enabling computational methods for studying large biological complexes initially through workshops and pilot studies. It is hoped that there will be opportunities for cross-talk between the C2BC and the "3D-EM" Network of Excellence.
A summary of the joint activities in finalising a data definitions dictionary for 3DEM was presented at the June 2005 Gordon Conference on Three Dimensional Electron Microscopy (http://www.grc.uri.edu/programs/2005/threed.htm).
This work has also had contributions in the form of a proposal for 3DEM Data Exchange Conventions Document, 'Common Conventions for Interchange and Archiving of Three-Dimensional Electron Microscopy Information in Structural Biology', by J.B.Heymann, M.Chagoyen and D.M.Belnap, in press, see http://www.ebi.ac.uk/msd-srv/docs/3dem/conventions_draft.pdf
A further 3DEM Workshop for software developers will be hosted by the EU-3dem NoE at the EBI in Cambridge (UK) from October 12-14, 2005 when developers will be encouraged to start using the dictionary terms in code and begin the process of automation in recording and archiving data.
The MSD and RCSB are part of the World Wide PDB (wwPDB) whose mission is to deliver a single consistent archive of macromolecular structure data. The EBI and RCSB are now expanding this collaboration by seeking additional funding to create a joint deposition system for EM map and coordinate data and to deliver this data in a consistent form.
Kim Henrick
Head Macromolecular Structure Database
European Bioinformatics Institute
Cambridge UK
Helen Berman
Director Protein Data Bank
Rutgers, the State University of New Jersey
USA