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Structure paper

TitleMediator structure and rearrangements required for holoenzyme formation.
Journal, issue, pagesNature, Vol. 544, Issue 7649, Page 196-201, Year 2017
Publish date2017--13
AuthorsKuang-Lei Tsai / Xiaodi Yu / Sneha Gopalan / Ti-Chun Chao / Ying Zhang / Laurence Florens / Michael P Washburn / Kenji Murakami / Ronald C Conaway / Joan W Conaway / Francisco J Asturias
External linksPubMed:28241144 / Publisher's page
MethodsEM (single particle)
Resolution4.4 - 7.8 A
Structure data

EMDB-8479:
Cryo-EM map of the transcriptional Mediator

EMDB-8480:
Cryo-EM map of the Mediator-RNAPII complex

PDB-5u0p:
Cryo-EM structure of the transcriptional Mediator

PDB-5u0s:
Cryo-EM structure of the Mediator-RNAPII complex

SourceSchizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /
KeywordsBinding Sites / Cryoelectron Microscopy / Holoenzymes / Med14 protein, S pombe / Mediator Complex / Models, Molecular / Protein Binding / Protein Conformation / Protein Subunits / RNA Polymerase II / Schizosaccharomyces / Schizosaccharomyces pombe Proteins / Structure-Activity Relationship / TRANSCRIPTION / transcription / transcriptional / Mediator / Head / Middle / Tail / Srb / RNA polymerase II / Med / TRANSCRIPTION/TRANSFERASE / RNA / Pol2 / activation / complex / TRANSCRIPTION-TRANSFERASE complex

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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

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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)

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EMN Papers

Database of articles cited by 3DEM data entries

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.: EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

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