8RV3 | pdb_00008rv3

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

PDB DOI: https://doi.org/10.2210/pdb8RV3/pdb

Classification: REPLICATION
Organism(s): Vibrio cholerae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-01-31 Released: 2025-02-12
Deposition Author(s): Garcia-Pino, A., Talavera Perez, A.
Funding Organization(s): European Research Council (ERC)

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

PubMed: 39779702 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-55598-9
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 42.58 kDa
Atom Count: 2,164
Modeled Residue Count: 252
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RctB	A, B	187	Vibrio cholerae	Mutation(s): 0 Gene Names: VC_A0002
UniProt
Find proteins for A0A0X1L1K5 (Vibrio cholerae (strain MO10)) Explore A0A0X1L1K5 Go to UniProtKB: A0A0X1L1K5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0X1L1K5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]