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- PDB-9p9a: DnaB complex binding with ssDNA and dTDP-AlFx -

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Basic information

Entry
Database: PDB / ID: 9p9a
TitleDnaB complex binding with ssDNA and dTDP-AlFx
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Replicative DNA helicase DnaB
KeywordsDNA BINDING PROTEIN / Helicase
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA 5'-3' helicase / 5'-3' DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / THYMIDINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLiu, C. / Eliason, W.K. / Berger, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2026
Title: Cellular replisomes are powered by flex-fuel motors for unwinding DNA.
Authors: Fahad Rashid / Sushil Pangeni / Chuan Liu / Harish Kumar / Gyeongtae Sun Moon / Qianyun Yan / Taekjip Ha / James M Berger /
Abstract: DNA replication relies on hexameric, ring-shaped helicases to unwind parental DNA for supporting fork progression over tens of thousands of base pairs. Oddly, biochemical studies have suggested that, ...DNA replication relies on hexameric, ring-shaped helicases to unwind parental DNA for supporting fork progression over tens of thousands of base pairs. Oddly, biochemical studies have suggested that, on their own, replicative helicases are rather limited motors that struggle to couple rapid movement to nucleotide turnover (typically believed to be solely ATP). Here, single-molecule studies reveal that when properly loaded, the Escherichia coli (E. coli) replicative helicase, DnaB, is a tremendously fast single-stranded DNA translocase that moves up to three times more rapidly than the replisome (3 knt/s). Translocation is highly processive, resistant to pulling force/high salt, and can displace short, 3'-tailed DNA duplexes without apparent changes in speed. Surprisingly, we find that the loader for DnaB, DnaC, can use any rNTP or dATP for depositing DnaB onto ssDNA and that the helicase itself also must hydrolyze nucleotide for stable loading. DnaB translocation also turns out to be supported by any r/dNTP, a property shown to extend to the eukaryotic CMG replicative helicase. Overall, the DNA unwinding engines that support cellular replisomes are highly indiscriminate of their fuel source, a feature that may be of utility during times when cells encounter nucleotide pool stress but have committed to DNA synthesis.
History
DepositionJun 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicative DNA helicase DnaB
B: Replicative DNA helicase DnaB
C: Replicative DNA helicase DnaB
D: Replicative DNA helicase DnaB
H: Replicative DNA helicase DnaB
F: Replicative DNA helicase DnaB
M: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,75422
Polymers308,1067
Non-polymers2,64715
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Replicative DNA helicase DnaB / DNA 5'-3' helicase DnaB


Mass: 50699.445 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: dnaB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X4C9, DNA 5'-3' helicase
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 3909.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: AlF4
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of DnaB with ssDNA and dTDP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154856 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213121
ELECTRON MICROSCOPYf_angle_d0.40317736
ELECTRON MICROSCOPYf_dihedral_angle_d10.1785058
ELECTRON MICROSCOPYf_chiral_restr0.0432036
ELECTRON MICROSCOPYf_plane_restr0.0032257

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