9GDO | pdb_00009gdo

Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Vibrio cholerae transcription complexes reveal how ToxR and TcpP recruit the RNA polymerase and activate virulence genes.

Alcaide-Jimenez, A.Canals, A.Baudin, F.Machon, C.Fabrega-Ferrer, M.Bantysh, O.Perez-Luque, R.Murciano, B.Mohammad, A.A.Rowse, M.J.Ferracciolo, J.M.Krukonis, E.S.Muller, C.W.Coll, M.

(2026) Sci Adv 12: eadx9680-eadx9680

  • DOI: https://doi.org/10.1126/sciadv.adx9680
  • Primary Citation of Related Structures:  
    9GDO, 9GDP, 9GDQ, 9GDR, 9GDS

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaC [auth G],
G [auth A],
H [auth B]
330Vibrio cholerae O395Mutation(s): 0 
Gene Names: rpoAVC0395_A2149VC395_2684
EC: 2.7.7.6
UniProt
Find proteins for A5F572 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F572 
Go to UniProtKB:  A5F572
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F572
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth C]1,341Vibrio cholerae O395Mutation(s): 0 
Gene Names: rpoBVC0395_A2730VC395_0371
EC: 2.7.7.6
UniProt
Find proteins for A5F3P5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F3P5 
Go to UniProtKB:  A5F3P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F3P5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth D]1,401Vibrio cholerae O395Mutation(s): 0 
Gene Names: rpoCVC0395_A2731VC395_0372
EC: 2.7.7.6
UniProt
Find proteins for A5F3P6 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F3P6 
Go to UniProtKB:  A5F3P6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F3P6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth E]90Vibrio cholerae O395Mutation(s): 0 
Gene Names: rpoZVC0395_A2281VC395_2821
EC: 2.7.7.6
UniProt
Find proteins for A5F4S8 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F4S8 
Go to UniProtKB:  A5F4S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F4S8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDI [auth F]621Vibrio cholerae O395Mutation(s): 0 
Gene Names: rpoDVC0395_A0044
UniProt
Find proteins for A0A0H3AJ64 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A0A0H3AJ64 
Go to UniProtKB:  A0A0H3AJ64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3AJ64
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
ompU promoter template DNA strandA [auth T]69Vibrio cholerae O395
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
ompU promoter non-template DNA strandB [auth N]69Vibrio cholerae O395
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2020-12141GB-100
Generalitat de CatalunyaSpain2021SGR00423

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-28
    Changes: Data collection, Database references