Electron Microscopy Data Bank

Abbreviation:EMDB

Recommended

General Information

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB was founded at EBI in 2002, under the leadership of Kim Henrick. Since 2007 it has been operated jointly by the PDBe, and the Research Collaboratory for Structural Bioinformatics (RCSB PDB) as a part of EMDataBank which is funded by a joint NIH grant to PDBe, the RCSB and the National Center for Macromolecular Imaging (NCMI).

Homepage https://www.ebi.ac.uk/pdbe/emdb/

Countries that developed this resource Austria , Belgium , Croatia , Czech Republic , Denmark , Finland , France , Germany , Greece , Hungary , Iceland , Israel , Italy , Lithuania , Luxembourg , Malta , Montenegro , Netherlands , Norway , Portugal , Republic of Ireland , Slovakia , Spain , Sweden , Switzerland , United Kingdom , United States

Created in 2002

Taxonomic range

All

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: EMDB; Electron Microscopy Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.651n9j; Last edited: March 27, 2020, 11:08 p.m.; Last accessed: Oct 24 2020 10:33 a.m.

This record is maintained by ardan

Record updated: March 27, 2020, 11:07 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.651n9j' by 'The FAIRsharing Team' at 23:07, 27 Mar 2020 (approved):

	'onto_disciplines' has been modified:
		Before:
			Biology
		After:
			Biology
			Epidemiology
			Virology
		Added:
			Epidemiology
			Virology
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.651n9j' by 'The FAIRsharing Team' at 14:30, 12 Feb 2020 (approved):

	'organizations' has been modified:
		Before:
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory|http://pdbe.org|Maintains
			RCSB PDB|http://www.rcsb.org|Maintains
		After:
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
			Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory|http://pdbe.org|Maintains
			RCSB PDB|http://www.rcsb.org|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:

	'supportLinks' has been modified:
		Before:
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/genealogy.html
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/emschema.html/
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/statistics_main.html
		After:
			FAQ|https://www.ebi.ac.uk/pdbe/emdb/faq
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/genealogy.html
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/emschema.html/
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/statistics_main.html
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/policies.html
		Added:
			FAQ|https://www.ebi.ac.uk/pdbe/emdb/faq
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/genealogy.html
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/emschema.html/
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/statistics_main.html
			online documentation|https://www.ebi.ac.uk/pdbe/emdb/policies.html
		Removed:
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/genealogy.html
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/emschema.html/
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/statistics_main.html

	'countries' has been modified:
		Before:
			United Kingdom
			United States
		After:
			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
			United Kingdom
			United States
		Added:
			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
		Removed:

	'tools' has been modified:
		Before:
			EM Validation Services||http://www.ebi.ac.uk/pdbe/emdb/validators.html/
			Test data||http://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||http://www.ebi.ac.uk/pdbe/emdb/validation/fsc/
			Tilt pair validation server||http://www.ebi.ac.uk/pdbe/emdb/validation/tiltpair/
		After:
			EM Validation Services||https://www.ebi.ac.uk/pdbe/emdb/validators.html/
			Test data||https://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||https://www.ebi.ac.uk/pdbe/emdb/validation/fsc/
			Tilt pair validation server||https://www.ebi.ac.uk/pdbe/emdb/validation/tiltpair/
		Added:
			EM Validation Services||https://www.ebi.ac.uk/pdbe/emdb/validators.html/
			Test data||https://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||https://www.ebi.ac.uk/pdbe/emdb/validation/fsc/
			Tilt pair validation server||https://www.ebi.ac.uk/pdbe/emdb/validation/tiltpair/
		Removed:
			EM Validation Services||http://www.ebi.ac.uk/pdbe/emdb/validators.html/
			Test data||http://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||http://www.ebi.ac.uk/pdbe/emdb/validation/fsc/
			Tilt pair validation server||http://www.ebi.ac.uk/pdbe/emdb/validation/tiltpair/

	'onto_disciplines' has been modified:
		Before:
			Biology
			Life Science
		After:
			Biology
		Added:
		Removed:
			Life Science

	'onto_domains' has been modified:
		Before:
			X-ray diffraction
			electron density map data
			electron microscopy
			microscopy
			structure
		After:
			Biological imaging
			X-ray diffraction
			electron density map data
			electron microscopy
			microscopy
			structure
		Added:
			Biological imaging
		Removed:

	'homepage' has been modified:
		Before: http://www.ebi.ac.uk/pdbe/emdb/
		After: https://www.ebi.ac.uk/pdbe/emdb/

Edits to 'https://fairsharing.org/FAIRsharing.651n9j' by 'The FAIRsharing Team' at 19:54, 20 Feb 2019 (approved):

	'tools' has been modified:
		Before:
			EM Validation Services||http://www.ebi.ac.uk/pdbe/emdb/validators.html/
			Test data||http://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||http://pdbe.org/fsc
			Tilt pair validation server||http://pdbe.org/tiltpair
		After:
			EM Validation Services||http://www.ebi.ac.uk/pdbe/emdb/validators.html/
			Test data||http://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||http://www.ebi.ac.uk/pdbe/emdb/validation/fsc/
			Tilt pair validation server||http://www.ebi.ac.uk/pdbe/emdb/validation/tiltpair/
		Added:
			Fourier shell correlation server||http://www.ebi.ac.uk/pdbe/emdb/validation/fsc/
			Tilt pair validation server||http://www.ebi.ac.uk/pdbe/emdb/validation/tiltpair/
		Removed:
			Fourier shell correlation server||http://pdbe.org/fsc
			Tilt pair validation server||http://pdbe.org/tiltpair

Edits to 'https://fairsharing.org/FAIRsharing.651n9j' by 'The FAIRsharing Team' at 19:52, 20 Feb 2019 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.emdatabank.org/faq.html
			email|help@emdatabank.org
			online documentation|http://www.emdatabank.org/cryoem_mapmodel_depguide.html
		After:
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/genealogy.html
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/emschema.html/
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/statistics_main.html
		Added:
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/genealogy.html
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/emschema.html/
			online documentation|http://www.ebi.ac.uk/pdbe/emdb/statistics_main.html
		Removed:
			FAQ|http://www.emdatabank.org/faq.html
			email|help@emdatabank.org
			online documentation|http://www.emdatabank.org/cryoem_mapmodel_depguide.html

	'licences' has been modified:
		Before:
		After:
			EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
		Added:
			EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
		Removed:

	'tools' has been modified:
		Before:
			EMDB statistics||http://pdbe.org/emstats
			Test data||http://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||http://pdbe.org/fsc
			Tilt pair validation server||http://pdbe.org/tiltpair
		After:
			EM Validation Services||http://www.ebi.ac.uk/pdbe/emdb/validators.html/
			Test data||http://www.ebi.ac.uk/pdbe/emdb/test_data.html
			Fourier shell correlation server||http://pdbe.org/fsc
			Tilt pair validation server||http://pdbe.org/tiltpair
		Added:
			EM Validation Services||http://www.ebi.ac.uk/pdbe/emdb/validators.html/
		Removed:
			EMDB statistics||http://pdbe.org/emstats

	'onto_disciplines' has been modified:
		Before:
			Life Sciences
		After:
			Biology
			Life Sciences
		Added:
			Biology
		Removed:

	'dataProcesses' has been modified:
		Before:
			Raw data archive
			Data submission
			Advanced search
			Search
			Browse archive
		After:
			Browse Latest Maps
			Data submission
			Advanced search
			Download (FTP)
			Browse
			Browse Latest Header Releases
			Browse Latest Updates
		Added:
			Browse Latest Maps
			Download (FTP)
			Browse
			Browse Latest Header Releases
			Browse Latest Updates
		Removed:
			Raw data archive
			Search
			Browse archive

	'onto_domains' has been modified:
		Before:
			X-ray diffraction
			electron density map data
			microscopy
			structure
		After:
			X-ray diffraction
			electron density map data
			electron microscopy
			microscopy
			structure
		Added:
			electron microscopy
		Removed:

	'yearOfCreation' has been modified:
		Before: 2011
		After: 2002

	'homepage' has been modified:
		Before: http://www.emdatabank.org/
		After: http://www.ebi.ac.uk/pdbe/emdb/

In Collections

Data Citation Implementation

EOSC-Life

ELIXIR Core Data Resources and Deposition Databases

COVID-19 Resources

RDA Covid-19 WG Resources

Support

General

FAQ	FAQ
online documentation	3DEM History and Genealogy
online documentation	EMDB Data Model
online documentation	EMDB Statistics
online documentation	Policies

Additional Information

Contact

Ardan Patwardhan ORCID

Tools

Test data	https://www.ebi.ac.uk/pdbe/emdb/test_data.html
Fourier shell correlation server	https://www.ebi.ac.uk/pdbe/emdb/validation/fsc/
Tilt pair validation server	https://www.ebi.ac.uk/pdbe/emdb/validation/tiltpair/
EM Validation Services	https://www.ebi.ac.uk/pdbe/emdb/validators.html/

Access / Retrieve Data

Conditions of Use

Applies to: Data use

EMBL-EBI Terms of Use

Data Release

Download (FTP)

ftp://ftp.ebi.ac.uk/pub/databases/emdb

Data Curation

Data submission

https://deposit-pdbe.wwpdb.org/deposition/

Data Access

Browse Latest Maps	https://www.ebi.ac.uk/pdbe/emdb/release/map/
Advanced search	https://www.ebi.ac.uk/pdbe/emdb/searchForm.html/
Browse	https://www.ebi.ac.uk/pdbe/emdb/browse.html/
Browse Latest Header Releases	https://www.ebi.ac.uk/pdbe/emdb/release/header/
Browse Latest Updates	https://www.ebi.ac.uk/pdbe/emdb/release/update/

Publications

EMDataBank.org: unified data resource for CryoEM

Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W.
Nucleic Acids Res. 2011

View Paper (PubMed) View Publication

New electron microscopy database and deposition system

Tagari, M. Newman, R. Chagoyen, M. Carazo, J. M. Henrick, K.
Trends in Biochemical Sciences 2002

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Credit

Record Maintainer

This record is maintained by ardan

Funds

National Institutes of Health (NIH), Bethesda, MD, USA (Government body)

Maintains

Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory (Research institute) Lead
RCSB PDB (Consortium) Lead
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)

Electron Microscopy Data Bank

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