9GD7 | pdb_00009gd7

DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural and functional insights into the interaction between Ku70/80 and Pol X family polymerases in NHEJ.

Frit, P.Amin, H.Zahid, S.Barboule, N.Hall, C.Matharu, G.Hardwick, S.W.Chauvat, J.Britton, S.Chirgadze, D.Y.Ropars, V.Charbonnier, J.B.Calsou, P.Chaplin, A.K.

(2025) Nat Commun 16: 4208-4208

  • DOI: https://doi.org/10.1038/s41467-025-59133-2
  • Primary Citation Related Structures: 
    9G9L, 9GD7, 9I04

  • PubMed Abstract: 

    Non-homologous end joining (NHEJ) is the main repair pathway for double-strand DNA breaks (DSBs) in mammals. DNA polymerases lambda (Pol λ) and mu (Pol μ), members of the Pol X family, play a key role in this process. However, their interaction within the NHEJ complexes is unclear. Here, we present cryo-EM structures of Pol λ in complex with the DNA-PK long-range synaptic complex, and Pol μ bound to Ku70/80-DNA. These structures identify interaction sites between Ku70/80 and Pol X BRCT domains. Using mutants at the proteins interface in functional assays including cell transfection with an original gap-filling reporter, we define the role of the BRCT domain in the recruitment and activity of the two Pol X members in NHEJ and in their contribution to cell survival following DSBs. Finally, we propose a unified model for the interaction of all Pol X members with Ku70/80.


  • Organizational Affiliation
    • Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), Toulouse, France.

Macromolecule Content 

  • Total Structure Weight: 903.85 kDa 
  • Atom Count: 41,717 
  • Modeled Residue Count: 5,208 
  • Deposited Residue Count: 7,881 
  • Unique protein chains: 7
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA ligase 4A [auth E]911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49917 (Homo sapiens)
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Go to UniProtKB:  P49917
PHAROS:  P49917
GTEx:  ENSG00000174405 
Entity Groups
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UniProt GroupP49917
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5B [auth L]732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4 (PDB Primary Data), 5.6.2.4 (UniProt), 4.2.99.18 (UniProt)
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Find proteins for P13010 (Homo sapiens)
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PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein PAXXC [auth M]204Homo sapiensMutation(s): 0 
Gene Names: PAXXC9orf142XLS
UniProt
Find proteins for Q9BUH6 (Homo sapiens)
Explore Q9BUH6 
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UniProt GroupQ9BUH6
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4D [auth P],
E [auth Q]
336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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Find proteins for Q13426 (Homo sapiens)
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PHAROS:  Q13426
GTEx:  ENSG00000152422 
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UniProt GroupQ13426
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunitF [auth S]4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78527 (Homo sapiens)
Explore P78527 
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PHAROS:  P78527
GTEx:  ENSG00000253729 
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UniProt GroupP78527
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6G [auth T]609Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data), 5.6.2.4 (UniProt), 4.2.99.18 (UniProt)
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Find proteins for P12956 (Homo sapiens)
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PHAROS:  P12956
GTEx:  ENSG00000196419 
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UniProt GroupP12956
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase lambdaJ [auth A]575Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5
GTEx:  ENSG00000166169 
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UniProt GroupQ9UGP5
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 7
MoleculeChains LengthOrganismImage
DNAH [auth i]25Homo sapiens
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Reference Sequence
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNAI [auth j]25Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/X00029X/1
The Lister Institute of Preventive MedicineUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Data collection, Database references