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- PDB-9vnq: Bacillus Subtilis Ku core homodimer complexed with double strand DNA -

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Basic information

Entry
Database: PDB / ID: 9vnq
TitleBacillus Subtilis Ku core homodimer complexed with double strand DNA
Components
  • (DNA (31-MER)) x 2
  • Non-homologous end joining protein Ku
KeywordsDNA BINDING PROTEIN / Non homologous end joining / DNA bridging
Function / homology
Function and homology information


double-strand break repair via nonhomologous end joining / double-stranded DNA binding / DNA recombination
Similarity search - Function
Non-homologous end joining protein Ku, prokaryotic type / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Non-homologous end joining protein Ku
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsKim, W.J. / Kim, M.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structure of Bacillus subtilis Ku-mediated DNA synaptic complex.
Authors: Whan-Jong Kim / Jieun Kim / Mingyu Jo / Youngjin Kim / Min-Sung Kim /
Abstract: DNA double-strand breaks (DSBs) pose a severe threat to genomic integrity, and cells rely on two major pathways for repair: homologous recombination and non-homologous end joining (NHEJ). While ...DNA double-strand breaks (DSBs) pose a severe threat to genomic integrity, and cells rely on two major pathways for repair: homologous recombination and non-homologous end joining (NHEJ). While eukaryotic NHEJ requires a multi-component assembly including the Ku70/80 heterodimer, bacterial NHEJ operates with a simpler toolkit comprising a Ku homodimer and the multifunctional LigD. Despite this simplicity, the mechanism by which broken DNA ends are bridged together has remained unclear in bacterial NHEJ. Here, we present a cryo-electron microscopy structure of the Bacillus subtilis Ku (bsKu)-DNA complex at 2.74 Å resolution, capturing two blunt DNA ends bridged by a Ku protein alone. Supported by further biochemical assays, we propose an integrated model in which oligomeric arrays of Ku homodimers bridge and stabilize two DNA ends, facilitating efficient DSB repair in Bacillus subtilis. This work reveals a bsKu-mediated DNA bridging mechanism distinct from the eukaryotic system and provides critical structural insight into prokaryotic DNA repair.
History
DepositionJun 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-homologous end joining protein Ku
B: Non-homologous end joining protein Ku
C: Non-homologous end joining protein Ku
D: Non-homologous end joining protein Ku
E: DNA (31-MER)
F: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)123,2746
Polymers123,2746
Non-polymers00
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
Non-homologous end joining protein Ku


Mass: 26052.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ku, ykoV, BSU13410 / Production host: Escherichia coli (E. coli) / References: UniProt: O34859
#2: DNA chain DNA (31-MER)


Mass: 9616.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (31-MER)


Mass: 9447.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: Bacillus Subtilis Ku core homodimer complexed with double strand DNA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156247 / Symmetry type: POINT

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