The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located.[2] As of 2015[update], the resource contained over 2,600 entries with a mean resolution of 15Å.[3]
Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into the wwPDB OneDep interface.[4]
Under the NIH Unified Data Resource for CryoEM, the Research Collaboration for Structural Biology (RCSB) also acts as a deposition, data processing and distribution center for EMDB data, while the National Center for Macromolecular Imaging (NCMI) is a collaborative partner in providing services and tools concerning the EMDB.
EM Data Bank also provides the EMsearch search tool and data can also be queried at RCSB, EMBL-EBI and PDBj.
EMDB is an archive for three-dimensional density maps of all types of biological assemblies, including ribosomes, chaperones, polymerases, multifunctional enzymes and viruses. Viper EMDB at Scripps is a separate database for three-dimensional EM maps of viruses.
To compare and assess methods for the new generation of higher resolution (better than 5Å) structures, the EMDB has hosted the first CryoEM Map Challenge and CryoEM Model Challenge, reported in a special issue of the Journal of Structural Biology.[5]
^Lawson, Catherine L; Baker, Matthew L; Best, Christoph; et al. (January 2011). "EMDataBank.org: unified data resource for CryoEM". Nucleic Acids Research. 39 (suppl 1): D456-464. doi:10.1093/nar/gkq880. PMC3013769. PMID 20935055.
^EMDB. "Electron Microscopy Data Bank". Electron Microscopy Data Bank. Retrieved 2021-08-05.
^Esquivel-Rodríguez, J; Xiong, Y; Han, X; et al. (30 May 2015). "Navigating 3D electron microscopy maps with EM-SURFER". BMC Bioinform.16 (181): 181. doi:10.1186/s12859-015-0580-6. PMC4448178. PMID 26025554.
^Young, JY; Westbrook, JD; Feng, Z; Sala, R; Peisach, E; Oldfield, TJ; Sen, S; Gutmanas, A; Armstrong, DR; Berrisford, JM; Chen, L; Chen, M; Di Costanzo, L; Dimitropoulos, D; Gao, G; Ghosh, S; Gore, S; Guranovic, V; Hendrickx, PM; Hudson, BP; Igarashi, R; Ikegawa, Y; Kobayashi, N; Lawson, CL; Liang, Y; Mading, S; Mak, L; Mir, MS; Mukhopadhyay, A; Patwardhan, A; Persikova, I; Rinaldi, L; Sanz-Garcia, E; Sekharan, MR; Shao, C; Swaminathan, GJ; Tan, L; Ulrich, EL; van Ginkel, G; Yamashita, R; Yang, H; Zhuravleva, MA; Quesada, M; Kleywegt, GJ; Berman, HM; Markley, JL; Nakamura, H; Velankar, S; Burley, SK (2017). "OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive". Structure. 25 (3): 536–545. doi:10.1016/j.str.2017.01.004. PMC5360273. PMID 28190782.
^Lawson, Catherine; Chiu, Wah, eds. (2018). "The CryoEM Structure Map and Model Challenges". Journal of Structural Biology. 204 (1). ISSN 1047-8477.
Tagari, Mohamed; Newman, Richard; Chagoyen, Monica; Carazo, Jose-Maria; Henrick, Kim (2002). "New electron microscopy database and deposition system". Trends in Biochemical Sciences. 27 (11): 589. doi:10.1016/s0968-0004(02)02176-x. PMID 12417136.
Fuller, Stephen D. (2003). "Depositing electron microscopy maps". Structure. 11 (1): 11–12. doi:10.1016/s0969-2126(02)00942-5. PMID 12517335.
Henrick, K; Newman, R; Tagari, M; Chagoyenb, M (2003). "EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information". Journal of Structural Biology. 144 (1–2): 228–237. doi:10.1016/j.jsb.2003.09.009. PMID 14643225.
Heymann, J. Bernard; Chagoyen, Mónica; Belnap, David M. (2005). "Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology". Journal of Structural Biology. 151 (2): 196–207. doi:10.1016/j.jsb.2005.06.001. PMID 16043364.
Tagari, M.; Tate, J.; Swaminathan, G. J.; et al. (2006). "E-MSD: improving data deposition and structure quality". Nucleic Acids Research. 34 (Database issue): 287–290. doi:10.1093/nar/gkj163. PMC1347525. PMID 16381867.
External linksedit
Software tools for molecular microscopy
EM Data Bank
US and UK Search pages
Japan Search page (EM Navigator in PDBj)
April 11, 2024
data, bank, electron, microscopy, data, bank, emdb, collects, maps, associated, experimental, data, determined, using, electron, microscopy, biological, specimens, established, 2002, pdbe, group, european, bioinformatics, institute, where, european, site, emda. The EM Data Bank or Electron Microscopy Data Bank EMDB collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens It was established in 2002 at the MSD PDBe group of the European Bioinformatics Institute EBI where the European site of the EMDataBank org consortium is located 2 As of 2015 update the resource contained over 2 600 entries with a mean resolution of 15A 3 EMDataBank orgContentDescriptionUnified Data Resource for CryoEM ContactResearch centerEuropean Bioinformatics Institute UK site AND Rutgers University USA site LaboratoryPDBe amp RCSB PDBPrimary citationLawson amp al 2011 1 Release date2002AccessWebsiteebi wbr ac wbr uk wbr emdbDeposition of data was originally via the EMdep deposition interface but since 2016 deposition of data has been incorporated into the wwPDB OneDep interface 4 Under the NIH Unified Data Resource for CryoEM the Research Collaboration for Structural Biology RCSB also acts as a deposition data processing and distribution center for EMDB data while the National Center for Macromolecular Imaging NCMI is a collaborative partner in providing services and tools concerning the EMDB EM Data Bank also provides the EMsearch search tool and data can also be queried at RCSB EMBL EBI and PDBj EMDB is an archive for three dimensional density maps of all types of biological assemblies including ribosomes chaperones polymerases multifunctional enzymes and viruses Viper EMDB at Scripps is a separate database for three dimensional EM maps of viruses To compare and assess methods for the new generation of higher resolution better than 5A structures the EMDB has hosted the first CryoEM Map Challenge and CryoEM Model Challenge reported in a special issue of the Journal of Structural Biology 5 See also editCryo Electron Microscopy Colocalization Benchmark SourceReferences edit Lawson Catherine L Baker Matthew L Best Christoph et al January 2011 EMDataBank org unified data resource for CryoEM Nucleic Acids Research 39 suppl 1 D456 464 doi 10 1093 nar gkq880 PMC 3013769 PMID 20935055 EMDB Electron Microscopy Data Bank Electron Microscopy Data Bank Retrieved 2021 08 05 Esquivel Rodriguez J Xiong Y Han X et al 30 May 2015 Navigating 3D electron microscopy maps with EM SURFER BMC Bioinform 16 181 181 doi 10 1186 s12859 015 0580 6 PMC 4448178 PMID 26025554 Young JY Westbrook JD Feng Z Sala R Peisach E Oldfield TJ Sen S Gutmanas A Armstrong DR Berrisford JM Chen L Chen M Di Costanzo L Dimitropoulos D Gao G Ghosh S Gore S Guranovic V Hendrickx PM Hudson BP Igarashi R Ikegawa Y Kobayashi N Lawson CL Liang Y Mading S Mak L Mir MS Mukhopadhyay A Patwardhan A Persikova I Rinaldi L Sanz Garcia E Sekharan MR Shao C Swaminathan GJ Tan L Ulrich EL van Ginkel G Yamashita R Yang H Zhuravleva MA Quesada M Kleywegt GJ Berman HM Markley JL Nakamura H Velankar S Burley SK 2017 OneDep Unified wwPDB System for Deposition Biocuration and Validation of Macromolecular Structures in the PDB Archive Structure 25 3 536 545 doi 10 1016 j str 2017 01 004 PMC 5360273 PMID 28190782 Lawson Catherine Chiu Wah eds 2018 The CryoEM Structure Map and Model Challenges Journal of Structural Biology 204 1 ISSN 1047 8477 Tagari Mohamed Newman Richard Chagoyen Monica Carazo Jose Maria Henrick Kim 2002 New electron microscopy database and deposition system Trends in Biochemical Sciences 27 11 589 doi 10 1016 s0968 0004 02 02176 x PMID 12417136 Fuller Stephen D 2003 Depositing electron microscopy maps Structure 11 1 11 12 doi 10 1016 s0969 2126 02 00942 5 PMID 12517335 Henrick K Newman R Tagari M Chagoyenb M 2003 EMDep a web based system for the deposition and validation of high resolution electron microscopy macromolecular structural information Journal of Structural Biology 144 1 2 228 237 doi 10 1016 j jsb 2003 09 009 PMID 14643225 Heymann J Bernard Chagoyen Monica Belnap David M 2005 Common conventions for interchange and archiving of three dimensional electron microscopy information in structural biology Journal of Structural Biology 151 2 196 207 doi 10 1016 j jsb 2005 06 001 PMID 16043364 Tagari M Tate J Swaminathan G J et al 2006 E MSD improving data deposition and structure quality Nucleic Acids Research 34 Database issue 287 290 doi 10 1093 nar gkj163 PMC 1347525 PMID 16381867 External links editSoftware tools for molecular microscopy EM Data Bank US and UK Search pages Japan Search page EM Navigator in PDBj Retrieved from https en wikipedia org w index php title EM Data Bank amp oldid 1188179759, wikipedia, wiki, book, books, library,
