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Yorodumi Species
- Taxonomy data in EMDB/PDB/SASBDB -

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Name, Taxonomy-ID, or Keywords:

e.g. E. coli, ebola, influenza, cow, crab-eating macaque, spinach, peanut, cobra, pyrococcus

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Result of keyword search

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Taxonomy info

NameEscherichia coli
Image *1Image

Escherichia coli, "Bacillus coli" Migula 1895, "Bacterium coli commune" Escherich 1885, Bacillus coli, Bacterium coli, Bacterium coli (Migula 1895) Lehmann and Neumann 1896, Bacterium coli commune, Escherichia coli (Migula 1895) Castellani and Chalmers 1919

Other names *2scientific name: Escherichia coli / common name: E. coli / synonym: Bacillus coli, Bacterium coli, Bacterium coli commune, Enterococcus coli / equivalent name: Escherichia/Shigella coli
Lineage *2cellular organisms > Bacteria > Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia
Yorodumi annotationbacteria
References*1: Taxonomy icon (c) Database Center for Life Science licensed under CC Attribution2.1 Japan
*2: NCBI Taxonomy
LinksNCBI taxonomy ID: 562

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EMDB entries

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PDB entries

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SASBDB entries

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About Yorodumi Species

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News

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

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Yorodumi Speices

Taxonomy data in EMDB/PDB/SASBDB

  • Taxonomy database of sample sources of data in EMDB/PDB/SASBDB

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks

Read more