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 9TZF | pdb_00009tzf

Vibrio cholerae DnaB-DciA open ring complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9TZF

This is version 1.0 of the entry. See complete history. 

Literature

Structural basis of DnaB ring opening by the ancestral helicase loader DciA.

Araujo-Bazan, L., Arias-Palomo, E.

(2026) Nucleic Acids Res 54

  • DOI: https://doi.org/10.1093/nar/gkag977
  • Primary Citation Related Structures: 
    9TZF

  • PubMed Abstract: 

    Ring-shaped helicases must be opened and loaded onto DNA to initiate genome replication. In bacteria, most species lack canonical AAA+ helicase loaders and instead rely on DciA, an evolutionarily conserved, ATP-independent factor whose mechanism has remained unclear. Here we define how DciA remodels the bacterial replicative helicase DnaB. A 3.5 Å cryo-EM structure reveals a DnaB6·DciA3 complex in which DciA binds the periphery of the helicase and stabilizes a right-handed open-helical conformation with a single cracked interface. Three DciA molecules dock onto alternate linker-helix/docking-helix modules, while one N-terminal domain (NTD) engages the cracked interface, occupying the pocket vacated by the displaced linker helix and acting as a wedge to promote ring opening. Functional analyses reveal how DciA couples ATPase suppression with efficient helicase loading through coordinated actions of its NTDs and C-terminal domains. Together, these findings define a minimal, ATP-independent mechanism for helicase loading and show how an ancestral loader remodels DnaB to overcome a fundamental topological barrier.


  • Organizational Affiliation: 
    • Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 368.08 kDa 
  • Atom Count: 22,544 
  • Modeled Residue Count: 2,870 
  • Deposited Residue Count: 3,279 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Replicative DNA helicase
A, B, C, D, E
A, B, C, D, E, F
468Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_0371
EC: 5.6.2.3
UniProt
Find proteins for Q9KUY7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KUY7 
Go to UniProtKB:  Q9KUY7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KUY7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF721 domain-containing protein
G, H, I
157Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_2395
UniProt
Find proteins for Q9KPH3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KPH3 
Go to UniProtKB:  Q9KPH3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KPH3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
S [auth E]
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2023-152248NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2026-11-04
    Type: Initial release