News Item:Joint European and United States 3D-EM Activities

emdep emdep at
Mon Jun 27 09:09:09 PDT 2005

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
( The latter project
established the first 3D Electron Microscopy deposition/archive system
(EMDep; and associated relational
database (EMdb; 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 and

The IIMS project started a series of workshops with many participants
from both Europe and the US (see for example

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 ( 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,

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; This workshop
was co-sponsored by the Computational Center for Biomolecular
Complexes (C2BC). The C2BC ( 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

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

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

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

 The EMD at EBI
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