9VNQ | pdb_00009vnq

Bacillus Subtilis Ku core homodimer complexed with double strand DNA

• PDB DOI: https://doi.org/10.2210/pdb9VNQ/pdb
• EM Map EMD-65215: EMDB EMDataResource
• NAKB: 9VNQ

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus subtilis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-30 Released: 2025-10-29 
• Deposition Author(s): Kim, W.J., Kim, M.S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Bacillus subtilis Ku-mediated DNA synaptic complex.

Kim, W.J., Kim, J., Jo, M., Kim, Y., Kim, M.S.

(2026) Nucleic Acids Res 54

• PubMed: 41118517 
• DOI: https://doi.org/10.1093/nar/gkaf1036
• Primary Citation of Related Structures:  
  9VNQ


• PubMed 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 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.

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Organizational Affiliation: 
• Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 123.27 kDa 
• Atom Count: 8,559 
• Modeled Residue Count: 967 
• Deposited Residue Count: 970 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-homologous end joining protein Ku	A, B, C, D	227	Bacillus subtilis	Mutation(s): 0  Gene Names: ku, ykoV, BSU13410
UniProt
Find proteins for O34859 (Bacillus subtilis (strain 168)) Explore O34859  Go to UniProtKB:  O34859

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	E	31	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	F	31	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Kim, W.J., Kim, M.S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release
  
• Version 1.1: 2026-01-21
  Changes: Data collection, Database references