29KM | pdb_000029km

Cryo-EM structure of Bacillus subtilis DnaB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Guyet, A.Campoy, R.R.Manja, P.Schramm, F.D.Pelliciari, S.Fenyk, S.Li, Y.Winterhalter, C.Ilangovan, A.Murray, H.

(2026) Nucleic Acids Res 54

  • DOI: https://doi.org/10.1093/nar/gkag630
  • Primary Citation Related Structures: 
    29KM

  • PubMed Abstract: 

    DNA replication is initiated at specific chromosomal loci termed origins. In bacteria, the master replication initiation protein DnaA unwinds the origin (oriC), allowing a pair of replicative helicases to be loaded around each strand of the DNA duplex. The molecular mechanisms for managing bacterial helicase loading at oriC are unclear. Here we have investigated the role of the essential accessory helicase loader DnaB in Bacillus subtilis. By identifying and characterizing DnaB residues that are critical for its role during DNA replication initiation, we have located three necessary protein-protein interactions that DnaB makes with initiation proteins DnaA, DnaD, and DnaI. Combining single particle cryo-electron microscopy, AlphaFold3 predictions, and two-hybrid interaction analyses, the data suggests that DnaB acts as an interaction hub to orchestrate dual helicase loading at the origin. We propose a model for DNA replication initiation in B. subtilis and related Firmicutes pathogens that employ DnaB-type helicase loaders.


  • Organizational Affiliation
    • Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne NE2 4AX, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 219.84 kDa 
  • Atom Count: 7,340 
  • Modeled Residue Count: 896 
  • Deposited Residue Count: 1,888 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Replicative helicase loading/DNA remodeling protein DnaB
A, B, C, D
472Bacillus subtilisMutation(s): 0 
Gene Names: dnaBBSU28990
UniProt
Find proteins for P07908 (Bacillus subtilis (strain 168))
Explore P07908 
Go to UniProtKB:  P07908
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07908
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom225811/Z/22/Z

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-15
    Type: Initial release