[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

TitleRapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation.
Journal, issue, pagesNat Struct Mol Biol, Year 2025
Publish dateJan 8, 2025
AuthorsJoshua J Brewer / Koe Inlow / Rachel A Mooney / Barbara Bosch / Paul Dominic B Olinares / Leandro Pimentel Marcelino / Brian T Chait / Robert Landick / Jeff Gelles / Elizabeth A Campbell / Seth A Darst /
PubMed AbstractFollowing transcript release during intrinsic termination, Escherichia coli RNA polymerase (RNAP) often remains associated with DNA in a post-termination complex (PTC). RNAPs in PTCs are removed from ...Following transcript release during intrinsic termination, Escherichia coli RNA polymerase (RNAP) often remains associated with DNA in a post-termination complex (PTC). RNAPs in PTCs are removed from the DNA by the SWI2/SNF2 adenosine triphosphatase (ATPase) RapA. Here we determined PTC structures on negatively supercoiled DNA and with RapA engaged to dislodge the PTC. We found that core RNAP in the PTC can unwind DNA and initiate RNA synthesis but is prone to producing R-loops. Nucleotide binding to RapA triggers a conformational change that opens the RNAP clamp, allowing DNA in the RNAP cleft to reanneal and dissociate. We show that RapA helps to control cytotoxic R-loop formation in vivo, likely by disrupting PTCs. We suggest that analogous ATPases acting on PTCs to suppress transcriptional noise and R-loop formation may be widespread. These results hold importance for the bacterial transcription cycle and highlight a role for RapA in maintaining genome stability.
External linksNat Struct Mol Biol / PubMed:39779919
MethodsEM (single particle)
Resolution3.62 - 4.69 Å
Structure data

40922

8szw

EMDB-40922, PDB-8szw:
Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: open duplex DNA (rPTCo)
Method: EM (single particle) / Resolution: 3.63 Å

40930

8t00

EMDB-40930, PDB-8t00:
Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc)
Method: EM (single particle) / Resolution: 4.69 Å

40931

8t02

EMDB-40931, PDB-8t02:
Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: unwinding duplex DNA (rPTCi)
Method: EM (single particle) / Resolution: 3.79 Å

40943

8t0l

EMDB-40943, PDB-8t0l:
E. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA
Method: EM (single particle) / Resolution: 3.62 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-AF3:
ALUMINUM FLUORIDE

Source
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsTRANSCRIPTION/DNA / RNA polymerase / Negatively supercoiled DNA / Sigma-independent transcription / TRANSCRIPTION-DNA complex / TRANSCRIPTION / RapA / RNAP recycling / Sw2/Snf2 ATPase

+
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