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- EMDB-57240: Cryo-EM structure of Bacillus subtilis DnaB -

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Basic information

Entry
Database: EMDB / ID: EMD-57240
TitleCryo-EM structure of Bacillus subtilis DnaB
Map dataDnaB unsharpened map
Sample
  • Organelle or cellular component: Bacillus subtilis DnaB
    • Protein or peptide: Replicative helicase loading/DNA remodeling protein DnaB
KeywordsApo DnaB structure / Bacillus subtilis DNA replication / Helicase loader / DNA BINDING PROTEIN
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA replication / DNA binding / plasma membrane / cytoplasm
Similarity search - Function
: / DnaB N-terminal winged helix domain / DnaD domain / DnaD-like domain superfamily / Replication initiation and membrane attachment
Similarity search - Domain/homology
Replicative helicase loading/DNA remodeling protein DnaB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCampoy RR / Guyet A / Pelliciari S / Murray H / Ilangovan A
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust225811/Z/22/Z United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.
Authors: Aurélie Guyet / Reyes Ruiz Campoy / Petra Manja / Frederic D Schramm / Simone Pelliciari / Stepan Fenyk / Yuanyuan Li / Charles Winterhalter / Aravindan Ilangovan / Heath Murray /
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 ...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.
History
DepositionMar 18, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57240.png

Downloads & links

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Map

FileDownload / File: emd_57240.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDnaB unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.21075241 - 0.46567133
Average (Standard dev.)0.00016493039 (±0.014731576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: DnaB half map B

Fileemd_57240_half_map_1.map
AnnotationDnaB half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DnaB half map A

Fileemd_57240_half_map_2.map
AnnotationDnaB half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus subtilis DnaB

EntireName: Bacillus subtilis DnaB
Components
  • Organelle or cellular component: Bacillus subtilis DnaB
    • Protein or peptide: Replicative helicase loading/DNA remodeling protein DnaB

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Supramolecule #1: Bacillus subtilis DnaB

SupramoleculeName: Bacillus subtilis DnaB / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Apo
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 104 KDa

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Macromolecule #1: Replicative helicase loading/DNA remodeling protein DnaB

MacromoleculeName: Replicative helicase loading/DNA remodeling protein DnaB
type: protein_or_peptide / ID: 1 / Details: DnaB chains A and D / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 54.96077 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADYWKDVLP VDPYVVKSRS MLQDIDRQII TQLYQPLIGP VAFSLYMTLW GELEQNRLWG GESTHRQLMG MTQSNLKTIH QEQGKLEGI GLLKVYMKES ERQERLFIYE LLPPLRPNEF FEDGMLNVFL YNRVGKTKYQ QLKQFFTHPA ISEDAKDITR P FNHAFESL ...String:
MADYWKDVLP VDPYVVKSRS MLQDIDRQII TQLYQPLIGP VAFSLYMTLW GELEQNRLWG GESTHRQLMG MTQSNLKTIH QEQGKLEGI GLLKVYMKES ERQERLFIYE LLPPLRPNEF FEDGMLNVFL YNRVGKTKYQ QLKQFFTHPA ISEDAKDITR P FNHAFESL QPSEWKLTSD MEETVRLAEG SEYTSVGQSP SYTITEDVFD FDLFLAGLSE TMIPRKAMTQ QVRDTIKKLS YL YGIDPLQ MQNVVMSAID ERDVITTEAL RKAASDWYQI ERNGQLPDLV EKTQPVHLRE GEQPAEEDSL DGKLIALLEA ISP KKLLQD IADGTEPSKA DLKIIEEIMF EQKLEPGVTN VLIYYVMLKT DMKLSKNYIQ KIASHWARKK VKTVREAMKL AIEE NRQYL EWAEGKTKSS KRNQKVIREE KLPDWMTEKE TASDSESGQQ KLHPQDLEEQ KKKMMEEMQK LKKYSAY

UniProtKB: Replicative helicase loading/DNA remodeling protein DnaB

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP / Details: Leica EM GP2.
DetailsApo DnaB

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 12516 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2578235
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Ab initio model generated de novo from the data and was used for particle curation and 3D refinement
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 144168
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 10 / Avg.num./class: 30000
Details: 3 classes were combined to form the final particle stack of 144168
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Residue range: 7-288 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: Truncated alphafold DnaB tetramer prediction
DetailsInitial rigid body fitting was done using Chimera X (Fit to Map). After retracing terminal residues, as well as rebuilding around Arg57, further modelling and real space refinement was used to refine the final model.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 139.5
Output model

PDB-29km:
Cryo-EM structure of Bacillus subtilis DnaB

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