[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 template strand deoxyuridine promoter recognition by a viral RNA polymerase.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 3526, Year 2022
Publish dateJun 20, 2022
AuthorsAlec Fraser / Maria L Sokolova / Arina V Drobysheva / Julia V Gordeeva / Sergei Borukhov / John Jumper / Konstantin V Severinov / Petr G Leiman /
PubMed AbstractRecognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template ...Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.
External linksNat Commun / PubMed:35725571 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.3 - 4.2 Å
Structure data

EMDB-24763: Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme in complex with DNA containing the AR9 P077 promoter
PDB-7um0: Structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with two DNA oligonucleotides containing the AR9 P077 promoter as determined by cryo-EM
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-24765: Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme
PDB-7um1: Structure of bacteriophage AR9 non-virion RNAP polymerase holoenzyme determined by cryo-EM
Method: EM (single particle) / Resolution: 4.1 Å

PDB-7s00:
X-ray structure of the phage AR9 non-virion RNA polymerase core
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-7s01:
X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the P077 promoter
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • bacillus phage ar9 (virus)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / DNA-dependent multisubunit RNA polymerase / deoxyuridine / template strand promoter / RNAP / TRANSCRIPTION/DNA / sigma factor / TRANSCRIPTION-DNA complex / template-strand promoter / sigma-like factor / gp226

+
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