[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 mechanism of ATP-independent transcription initiation by RNA polymerase I.
Journal, issue, pagesElife, Vol. 6, Year 2017
Publish dateJun 17, 2017
AuthorsYan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He /
PubMed AbstractTranscription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a ...Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.
External linksElife / PubMed:28623663 / PubMed Central
MethodsEM (single particle)
Resolution3.7 - 6.9 Å
Structure data

8771

5w5y

EMDB-8771, PDB-5w5y:
RNA polymerase I Initial Transcribing Complex
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-8772:
Core Factor local refinement from Pol I Initial Transcribing Complex at 4.2 angstrom
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-8773:
Pol I local refinement from Pol I Initial Transcribing Complex at 3.7 angstrom
Method: EM (single particle) / Resolution: 3.7 Å

8774

5w64

EMDB-8774, PDB-5w64:
RNA Polymerase I Initial Transcribing Complex State 1
Method: EM (single particle) / Resolution: 4.2 Å

8775

5w65

EMDB-8775, PDB-5w65:
RNA polymerase I Initial Transcribing Complex State 2
Method: EM (single particle) / Resolution: 4.3 Å

8776

5w66

EMDB-8776, PDB-5w66:
RNA polymerase I Initial Transcribing Complex State 3
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-8777:
Pol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom
Method: EM (single particle) / Resolution: 6.9 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • Baker's yeast (brewer's yeast)
KeywordsTRANSCRIPTION / RNA Polymerase I Core Factor Transcription

+
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