[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 Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 9990, Year 2025
Publish dateNov 13, 2025
AuthorsJoshua Brewer / Madeleine Delbeau / Winston Bates Zoullas / Seth A Darst / Elizabeth A Campbell /
PubMed AbstractTranscription in bacteria is a multi-step process. In the first step, contacts between RNA polymerase and the promoter DNA must be established for transcription initiation to begin, but then these ...Transcription in bacteria is a multi-step process. In the first step, contacts between RNA polymerase and the promoter DNA must be established for transcription initiation to begin, but then these contacts must be broken for the enzyme to transition into the elongation phase. Single-molecule and biochemical observations report that promoter escape is a highly regulated and sometimes rate-limiting step in the transcription cycle; however, the structural mechanisms of promoter escape remain obscure. Promoter escape also serves as the target for the clinically important antibiotic rifampicin, used to treat tuberculosis. Here, we present seven distinct intermediates showing the structural details of M. tuberculosis RNA polymerase initial transcribing complexes and promoter escape, using a de novo cryo-electron microscopy approach. We describe the structural rearrangements that RNA polymerase undergoes to clear the promoter, including those required to release the initiation factor, σ, providing a structural account for decades of biochemical observations. These structures and supporting biochemistry provide a model of promoter escape, a universal step in the transcription cycle, with conformations that may be used to develop Rifampicin alternatives.
External linksNat Commun / PubMed:41233305 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 4.2 Å
Structure data

47692

9e7v

EMDB-47692, PDB-9e7v:
Off-pathway Mycobacterium tuberculosis transcription initiation promoter complex (RNA Polymerase with Sigma-A, CarD, and RbpA)
Method: EM (single particle) / Resolution: 3.4 Å

47695

9e7y

EMDB-47695, PDB-9e7y:
De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 7-mer RNA and disordered Beta' Lid element (RNA Polymerase with Sigma-A, CarD, and RbpA)
Method: EM (single particle) / Resolution: 4.2 Å

47706

9e84

EMDB-47706, PDB-9e84:
De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 6-mer RNA and disordered Sigma-A region 4 domain (RNA Polymerase with Sigma-A, CarD, and RbpA)
Method: EM (single particle) / Resolution: 3.6 Å

47707

9e85

EMDB-47707, PDB-9e85:
De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 6-mer RNA and closed Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA)
Method: EM (single particle) / Resolution: 3.1 Å

47708

9e86

EMDB-47708, PDB-9e86:
De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 5-mer RNA and open Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA)
Method: EM (single particle) / Resolution: 3.8 Å

47709

9e87

EMDB-47709, PDB-9e87:
De Novo Mycobacterium tuberculosis transcription initiation pre-RPO promoter complex with open Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA)
Method: EM (single particle) / Resolution: 3.6 Å

47710

9e88

EMDB-47710, PDB-9e88:
De novo backtracked transcription elongation complex of Mycobacterium tuberculosis RNA polymerase on a linear DNA fragment (TEC-Backtracked)
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-POP:
PYROPHOSPHATE 2-

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • mycobacterium tuberculosis (bacteria)
  • synthetic construct (others)
Keywordstranscription/DNA / Promoter escape / transcription / transcription-DNA complex / TRANSCRIPTION/DNA/RNA / De novo / RNA polymerase / TRANSCRIPTION-DNA-RNA complex

+
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