8VF2 | pdb_00008vf2

CryoEM structure of Ku homodimer super-complex with linear DNA

• PDB DOI: https://doi.org/10.2210/pdb8VF2/pdb
• EM Map EMD-43184: EMDB EMDataResource
• NAKB: 8VF2

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): saltans group, Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-21 Released: 2025-12-10 
• Deposition Author(s): Baral, J., Rouiller, I., Das, A.K.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

First cryoEM structure of bacterial Ku in complex with DNA

Baral, J., Rouiller, I., Das, A.K.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 250.92 kDa 
• Atom Count: 13,357 
• Modeled Residue Count: 1,477 
• Deposited Residue Count: 1,930 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-homologous end joining protein Ku	C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F]	295	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: mku, Rv0937c
UniProt
Find proteins for P9WKD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD9  Go to UniProtKB:  P9WKD9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	A [auth I], I [auth G]	40	saltans group

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	B [auth J], J [auth H]	40	saltans group

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Baral, J., Rouiller, I., Das, A.K.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP2000934
Science and Engineering Research Board (SERB)	India	CRG/2020/002622

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release