The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project have collaborated to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive. With this work now completed, all 3DEM-derived entries have better-organized content and conform to the revised data model developed by the EMDataBank team for use within the wwPDB OneDep System.
The Assessment Phase of the EMDataBank Map Challenge is now officially open, and all are welcome to participate. The Challenge Phase (July 2015-Apr 2016) was a tremendous success, with 66 submitted maps spread across the 7 image data benchmark targets.
The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project (https://www.ncbi.nlm.nih.gov/pubmed/26578576) are collaborating to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive.
The new wwPDB Validation Server at https://validate.wwpdb.org now generates preliminary validation reports for structures solved by NMR and 3D Electron Microscopy, in addition to X-ray crystallography.
Announcement: Map Volume Deposition to EMDB Will Be Mandatory for PDB Depositions of 3DEM models Starting September 6th, 2016
Effective September 6th, 2016, deposition to the PDB of atomic models determined by 3D Electron cryo-Microscopy (3DEM) will require prior or simultaneous deposition of the associated 3DEM volume maps to EMDB.
The wwPDB Partners and the EMDataBank are pleased to announce that validation reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive have been publicly released.
Starting May 31st 2016, the legacy deposition systems EMDep, AutoDep, and EM-ADIT will no longer accept new EMDB and PDB submissions. Depositors with in-progress sessions on the legacy systems will be able to access and complete their deposition sessions until September 30th 2016.
The wwPDB Partners and the EMDataBank are pleased to announce that validation reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive will become publicly available in May.
The second International Conference on Image Analysis in Three-dimensional Cryo-EM, will be held at Granlibakken Conference Center, Lake Tahoe, California from March 30 to April 2, 2016. The second workshop in this series will again focus on cutting edge techniques for image analysis in Cryo-EM.
The wwPDB partners and the EMDataBank project are pleased to announce the launch of a new Deposition & Annotation system that supports structures determined using 3DEM, NMR, and X-ray, neutron and electron crystallography.
New open access articles about EMDataBank and EMDB access are now available online, in advance of publication in the upcoming January 2016 Nucleic Acids Research Database Issue.
Nov 9, 2015: We have two major announcements regarding the ongoing EMDataBank Map Challenge.
All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.
All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.
EMPIAR (Electron Microscopy Pilot Image ARchive; http://pdbe.org/empiar) is a public archive for raw image data (micrographs, particles, and tilt-series) related to EMDB entries. Important uses of EMPIAR data include validation and as test-data for methods development and teaching.
The PDBe tilt-pair validation web-server is now available from: http://www.pdbe.org/tiltpair. You can use this service to perform a tilt-pair analysis on your own data.
The EMDB team at the Protein Data Bank in Europe (PDBe) has two vacancies for scientific programmers to work on an exciting new MRC and BBSRC funded project to help bridge the worlds of cellular and molecular structural biology.
June 2014: EMDataBank Partner PDBe was recently awarded funding by MRC and BBSRC to set up a public archive for raw image data (micrographs, particles, and tilt-series) related to EMDB entries. The archive currently contains 7 datasets related to EMDB map entries, including a few multi-frame direct electron detector datasets.
EMDataBank Partner PDBe (EBI) and their collaborators at the Science & Technology Facilities Council in Daresbury are developing a web service as part of the BioMedBridges project that will enable the EMDB and PDB archives to be searched on the basis of 3D volumetric shape matching, rather than solely on the basis of metadata and/or coordinate models. The PDBe/STFC Biomedbridges team requests your input on 3D volume segmentation, which in many cases will be a necessary step before volume matching.
A record number of EM structural data entries were released in 2013: 544 EMDB maps, and 236 EM-PDB models. The overall size of the EM structural data archives has also substantially increased.
The first International Conference on Image Analysis in Three-dimensional Cryo-EM, to be held at Granlibakken Conference Center, Lake Tahoe, California from March 12 to March 15, 2014.
The goal of the Symposium is to discuss state of the art image analysis approaches to tackle challenging biological problems and to identify current limitations and remaining problems in the field as currently practiced.
Recent improvements to web-based visualisation and analysis of 3DEM data from EMDB and PDB are described in an open access article published in the November issue of the Journal of Structural Biology.
We have created a short online poll to collect your opinions about a possible change to EMDB data release policy.
Should complete experimental metadata associated with EMDB map entries continue to be available/searchable prior to map release?
The use of 3D cryo-electron microscopy reconstruction (3DEM) methods to experimentally determine structures of biological macromolecules, complexes and machines is rapidly increasing in the structural biology community. For journal articles reporting new 3DEM structures via single particle, helical, electron crystallography, and sub-tomogram averaging methods, we find that the overall map-deposition rate to EM Data Bank (EMDB) is approaching 70%. However, the rate varies significantly per journal, and tends to be highest for journals with well-defined and consistently enforced 3DEM deposition policies in place.
In order to meet the challenges of ever greater numbers of PDB depositions, involving ever larger and more complex structures, often determined using multiple methods, the Worldwide Protein Data Bank partners (wwPDB; http://wwpdb.org/) are developing a completely new system for deposition and annotation of PDB entries.
On 16 January 2013, the EMDB archive plans to adopt an updated format, v.1.9.0, for the entry header file (XML file associated with each map). This means that EMDB header files distributed from wwPDB partner sites will conform to the 1.9.0 format, and EMDataBank deposition/annotation/search services will start using this format.
As we announced early in the year, the EMDB map archive is now distributed alongside the PDB archive by all three wwPDB partner sites. To download or retrieve EMDB map or header files, please go to one of the three current distribution sites.
The September 2012 special issue of Biopolymers "2010 Cryo-EM Modeling Challenge" is now online. The issue contents include an editorial and eight articles describing results from the 2010 cryo-EM modeling challenge.
Every now and then depositors of EM data approach us with questions (or gripes) about the deposition process, in particular when both a map and a model are to be deposited.
Tomographic data deposition was the main topic of an informal afternoon meeting at the 2012 3DEM GRC that drew ~20 conferees.
A new MRC Partnership grant to provide computational support for UK scientists using electron cryo-microscopy for structural biology will aim to create a new Collaborative Computational Project, CCP-EM. Two excellent, motivated computational scientists are sought to support the Partnership grant and CCP-EM project. For details please view the full announcement here.
7-March-2012: The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, has joined the PDB archive (ftp://ftp.wwpdb.org), as announced previously.
We are pleased to announce the publication of the outcome of the first Electron Microscopy Validation Task Force (EM VTF) meeting in the journal Structure: Henderson et al., Structure (2012).
The 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods will be held March 14-18, 2012 in Lake Tahoe, CA.
The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, will join the PDB archive on 7 March 2012.
We are pleased to announce improved 3D web-based viewing of maps and associated coordinate models from EMDataBank atlas pages. The molecular visualization program OpenAstexViewer has been adapted by the EMDataBank team to display EM maps and their associated coordinate models.
In October 2011, the Worldwide Protein Data Bank (wwPDB) will host a scientific symposium celebrating the 40th anniversary of the inception of the PDB, and the many scientific contributions it archives. The program will showcase the scientific impact made by structural biology during the past 40 years with a distinguished panel of scientists who have been instrumental in the development of the PDB and structural biology.
A special issue of Biopolymers will cover the results of the first Cryo-EM Modeling Challenge held in 2010 with accompanying workshop at PSB 2011. The challenge was very successful with 136 models submitted by 10 different research groups using 13 different software packages.
February 2011: Congratulations are in order to the cryoEM community for reaching a significant milestone: more than 1000 maps representing a wide variety of biological assemblies are now archived in the EM DataBank.
Effective January 2011, the option to hold EM map volumes for two years before release to the public will no longer be available.
Up-to-date information about EMDataBank.org including history, current status, and future plans can be found in two publications now available online and in press.
September 2010: We are pleased to announce that a more uniform set of maps is now available through EMDataBank.org search services and ftp mirror sites.
July 2010: The Protein Data Bank in Europe (PDBe; pdbe.org) has a vacancy for the Project Leader Electron Microscopy position.
2010 Cryo-EM Modeling Challenge and PSB 2011 workshop organized by Steven Ludtke, Wah Chiu, Helen Berman and Gerard Kleywegt.
June 2010: The EmDataBank.org team is nearing completion of a major project to improve uniformity, viewability and useability of the 730+ map volumes in the EMDB that are currently available for download. Please read on to learn more about this project, and how to access the remediated maps.
You may have noticed that the emdatabank.org site is updated on a weekly basis. EMDB's weekly release cycle is also now synchronized with wwPDB's release cycle.
You have a brand new cryoEM density map of a biological assembly and want to generate a realistic coordinate model that fits the density. How should you proceed? This was the primary topic of discussion at the Modelling of CryoEM maps workshop held at the University of Houston on January 14-18, 2010.
The Workshop on Advanced Topics in EM Structure Determination: Challenging Molecules held Nov 8-13, 2009 at the National Resource for Automated Molecular Microscopy (NRAMM) at the Scripps Research Institute, was an intellectually stimulating meeting with over 100 attendees and an outstanding set of instructors. The meeting featured extensive discussion of challenges faced using cryoEM to solve macromolecules that are either small or conformationally variable in structure...
7 October 2009: This morning, the recipients of the 2009 Nobel Prize for Chemistry were announced. V. Ramakrishnan, T. A. Steitz, and A. E. Yonath will share the award for their studies on the structure and function of the ribosome.
Christoph Best (PDBe) gave a presentation on how to deposit and retrieve data sets in the EMDB at the 10-day EMBO Course in Cryo-Electron Microscopy at Birkbeck College, London organized by Elena Orlova and Helen Saibil.
The 2009 3DEM Gordon Research Conference in New London, NH was an exciting meeting with a full roster of excellent presentations and ample time for informal discussions. EMDataBank.org team members Christoph Best (PDBe) and Cathy Lawson (RCSB-PDB) presented a poster describing recent progress towards creating a unified data resource for cryoEM
March 2009: We are pleased to announce improvements to EM Databank deposition and retrieval services hosted by PDBe (Europe) and RCSB PDB (USA).
An open access article published in the August 2008 issue of Acta Crystallographica Section D describes the new scheme used by the PDB to archive regular non-crystallographic symmetry information for large biological assemblies.
Feb 2008: Electron microscopy map data can now be deposited to the EMDB using the improved web-based tool EmDep2.
Jan 2008: An informal one day workshop organized by Wah Chiu and Cathy Lawson was held on Jan 15, 2008 at the UCSF Mission Bay Campus.
Aug 2007: An NIH/NIGMS-funded collaboration to create a unified data resource for large complexes determined by cryo-electron microscopy has been established between the Macromolecular Structure Database Group at the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics at Rutgers, and the National Center for Macromolecular Imaging at Baylor College of Medicine.Read more
In order to develop a community data resource, it is necessary to solicit input from representative members of the scientific community. Below is a summary of past workshops devoted to exchange of cryoEM data that have been organized by members of our project group and other leaders in cryoEM.
Nov 2002, IIMS Workshop, organized by Kim Henrick, Jose-Maria Carazo (Madrid), and Stephen Fuller (Oxford), held at Hinxton, Cambridge, UK, workshop reportRead more