[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis of a transcription pre-initiation complex on a divergent promoter.
Journal, issue, pagesMol Cell, Vol. 83, Issue 4, Page 574-588.e11, Year 2023
Publish dateFeb 16, 2023
AuthorsJose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami /
PubMed AbstractMost eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single ...Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
External linksMol Cell / PubMed:36731470 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution3.3 - 36.0 Å
Structure data

26542

7ui9

EMDB-26542, PDB-7ui9:
Core Mediator-PICearly (Copy A)
Method: EM (single particle) / Resolution: 3.3 Å

26543

7uic

EMDB-26543, PDB-7uic:
Mediator-PIC Early (Tail A)
Method: EM (single particle) / Resolution: 3.7 Å

26544

7uif

EMDB-26544, PDB-7uif:
Mediator-PIC Early (Core B)
Method: EM (single particle) / Resolution: 4.6 Å

26545

7uig

EMDB-26545, PDB-7uig:
Mediator-PIC Early (Mediator A)
Method: EM (single particle) / Resolution: 4.3 Å

26547

7uik

EMDB-26547, PDB-7uik:
Mediator-PIC Early (Tail A + Upstream DNA & Activator)
Method: EM (single particle) / Resolution: 7.7 Å

26548

7uil

EMDB-26548, PDB-7uil:
Mediator-PIC Early (Tail A/B Dimer)
Method: EM (single particle) / Resolution: 4.3 Å

26551

7uio

EMDB-26551, PDB-7uio:
Mediator-PIC Early (Composite Model)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-28023: Dimerized Mediator-PIC with early GTFs and TFIIE on a divergent promoter
Method: EM (subtomogram averaging) / Resolution: 26.0 Å

EMDB-28024: Dimerized Mediator PIC with early GTFs on a divergent promoter
Method: EM (subtomogram averaging) / Resolution: 36.0 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-THR:
THREONINE

ChemComp-ALA:
ALANINE

ChemComp-ASP:
ASPARTIC ACID

Source
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsTRANSCRIPTION / Divergent transcription / Mediator / RNA Polymerase II / PIC / Pre-Initiation / Activation / Transcription Factor / Gal4 / Gal4VP16

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more