7QXM

Crystal structure of the Vibrio cholerae replicative helicase (DnaB)

• PDB DOI: https://doi.org/10.2210/pdb7QXM/pdb

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


• Deposited: 2022-01-26 Released: 2022-05-25 
• Deposition Author(s): Legrand, P., Quevillon-Cheruel, S., Walbott, H., Cargemel, C.
• Funding Organization(s): French Infrastructure for Integrated Structural Biology (FRISBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.266 
• R-Value Observed: 0.266 

Literature

The apo-form of the Vibrio cholerae replicative helicase DnaB is a labile and inactive planar trimer of dimers.

Cargemel, C., Walbott, H., Durand, D., Legrand, P., Ouldali, M., Ferat, J.L., Marsin, S., Quevillon-Cheruel, S.

(2022) FEBS Lett 596: 2031-2040

• PubMed: 35568982 
• DOI: https://doi.org/10.1002/1873-3468.14403
• Primary Citation of Related Structures:  
  7QXM


• PubMed Abstract: 
  

  To enable chromosomal replication, DNA is unwound by the ATPase molecular motor replicative helicase. The bacterial helicase DnaB is a ring-shaped homo-hexamer whose conformational dynamics are being studied through its different 3D structural states adopted along its functional cycle. Our findings describe a new crystal structure for the apo-DnaB from Vibrio cholerae, forming a planar hexamer with pseudo-symmetry, constituted by a trimer of dimers in which the C-terminal domains delimit a triskelion-shaped hole. This hexamer is labile and inactive. We suggest that it represents an intermediate state allowing the formation of the active NTP-bound hexamer from dimers.

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Organizational Affiliation: 

CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 317.63 kDa 
• Atom Count: 20,679 
• Modelled Residue Count: 2,651 
• Deposited Residue Count: 2,844 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicative DNA helicase	A, B, C, D, E, F	474	Vibrio cholerae	Mutation(s): 0  Gene Names: dnaB, BC353_11625, C9J66_17780, ERS013165_03687, ERS013200_03939, ERS013206_03692, F0315_03560, FLM02_14585, HPY05_12185 EC: 3.6.4.12
UniProt
Find proteins for A0A085R2T8 (Vibrio cholerae) Explore A0A085R2T8  Go to UniProtKB:  A0A085R2T8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.266 
• R-Value Observed: 0.266 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.23	α = 90
b = 150.099	β = 90
c = 188.264	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Legrand, P., Quevillon-Cheruel, S., Walbott, H., Cargemel, C.

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Funding Organization	Location	Grant Number
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INBS-05

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2022-09-07
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description