8RV3 | pdb_00008rv3

Structure of the domain IV of the replication factor RctB from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.267 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae.

Niault, T.Talavera, A.Le Cam, E.Baconnais, S.Skovgaard, O.Fournes, F.Wagner, L.Tamman, H.Thompson, A.Echemendia-Blanco, D.Guzzi, N.Garcia-Pino, A.Mazel, D.Val, M.E.

(2025) Nat Commun 16: 485-485

  • DOI: https://doi.org/10.1038/s41467-024-55598-9
  • Primary Citation of Related Structures:  
    8RV3

  • PubMed Abstract: 

    The replication of the two chromosomes in the pathogenic bacterium Vibrio cholerae is coordinated by the binding of initiator protein RctB to a checkpoint sequence, crtS. Replication of crtS on the primary chromosome (Chr1) triggers replication of the secondary chromosome (Chr2), but the details are poorly understood. Here, we analyze RctB binding patterns in the V. cholerae genome across various cell cycle stages. We find that RctB primarily binds to sites inhibiting replication initiation at the Chr2 origin (ori2). This inhibitory effect is counteracted when crtS is replicated on Chr1, causing a shift in RctB binding to sites that activate replication at ori2. Structural analyzes indicate the formation of diverse oligomeric states of RctB, coupled to the allosteric effect of DNA, which determine ori2 accessibility. We propose a synchronization model where, upon replication, crtS locally destabilizes the RctB inhibition complex, releasing the Chr2 replication origin.


  • Organizational Affiliation
    • Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RctB
A, B
187Vibrio choleraeMutation(s): 0 
Gene Names: VC_A0002
UniProt
Find proteins for A0A0X1L1K5 (Vibrio cholerae (strain MO10))
Explore A0A0X1L1K5 
Go to UniProtKB:  A0A0X1L1K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X1L1K5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth B]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.267 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.91α = 90
b = 94.76β = 90
c = 47.59γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union864311

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Database references