9GDP image
Deposition Date 2024-08-06
Release Date 2025-12-17
Last Version Date 2026-01-28
Entry Detail
PDB ID:
9GDP
Keywords:
Title:
Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment and 5-mer RNA
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Gene (Uniprot):rpoA
Chain IDs:D (auth: A), E (auth: B), H (auth: G)
Chain Length:330
Number of Molecules:3
Biological Source:Vibrio cholerae O395
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:A (auth: C)
Chain Length:1341
Number of Molecules:1
Biological Source:Vibrio cholerae O395
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Gene (Uniprot):rpoC
Chain IDs:B (auth: D)
Chain Length:1401
Number of Molecules:1
Biological Source:Vibrio cholerae O395
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:C (auth: E)
Chain Length:90
Number of Molecules:1
Biological Source:Vibrio cholerae O395
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase sigma factor RpoD
Gene (Uniprot):rpoD
Chain IDs:F
Chain Length:621
Number of Molecules:1
Biological Source:Vibrio cholerae O395
Polymer Type:polyribonucleotide
Molecule:RNA 5-mer (5'-AAUAG-3')
Chain IDs:G (auth: H)
Chain Length:5
Number of Molecules:1
Biological Source:Vibrio cholerae O395
Polymer Type:polydeoxyribonucleotide
Molecule:ompU promoter template DNA strand
Chain IDs:J (auth: L)
Chain Length:69
Number of Molecules:1
Biological Source:Vibrio cholerae O395
Polymer Type:polydeoxyribonucleotide
Molecule:ompU promoter non-template DNA strand
Chain IDs:I (auth: T)
Chain Length:69
Number of Molecules:1
Biological Source:Vibrio cholerae O395
Primary Citation
Structures of Vibrio cholerae transcription complexes reveal how ToxR and TcpP recruit the RNA polymerase and activate virulence genes.
Sci Adv 12 eadx9680 eadx9680 (2026)
PMID: 41533787 DOI: 10.1126/sciadv.adx9680

Abstact

Activation of virulence in Vibrio cholerae, the etiological agent of cholera disease, is mediated by two transmembrane one-component signal-transduction proteins, ToxR and TcpP, which are also transcription factors. Using cryo-electron microscopy, we have solved five structures of the ompU and toxT transcription activation complexes, including the RNA polymerase (RNAP) holoenzyme, promoter DNAs, transcribed RNA, and their corresponding transcription factors, ToxR or TcpP and ToxR-TcpP, respectively. Activation is achieved through the interaction of ToxR or TcpP with the α-C-terminal repeat domain of RNAP where a single residue of the activator, a phenylalanine, appears to be the most critical contact, as confirmed by mutagenesis. No interactions of the transcription factors were observed with other subunits of the RNAP, i.e., the σ subunit as it occurs in the structurally related PhoB family of two-component transcription factors. The structures, and their comparison with our previously solved DNA promoter-ToxR x-ray structures, unveil the molecular mechanism of cholera virulence gene activation.

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Primary Citation of related structures
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