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


This is version 1.0 of the entry. See complete history. 


Literature

Ku70/80 anchors DNA polymerase Lambda at sites of DNA synapsis during NHEJ

Chaplin, A.K., Amin, H., Zahid, S., Hardwick, S.W.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4A [auth E]911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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Find proteins for P49917 (Homo sapiens)
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PHAROS:  P49917
GTEx:  ENSG00000174405 
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UniProt GroupP49917
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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: XRCC5, G22P2
EC: 3.6.4
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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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PAXXC [auth M]204Homo sapiensMutation(s): 0 
Gene Names: PAXX, C9orf142, XLS
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GTEx:  ENSG00000148362 
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UniProt GroupQ9BUH6
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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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PHAROS:  Q13426
GTEx:  ENSG00000152422 
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UniProt GroupQ13426
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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
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Find proteins for P78527 (Homo sapiens)
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PHAROS:  P78527
GTEx:  ENSG00000253729 
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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: XRCC6, G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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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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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)
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Find proteins for Q9UGP5 (Homo sapiens)
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PHAROS:  Q9UGP5
GTEx:  ENSG00000166169 
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNAH [auth i]25Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNAI [auth j]25Homo sapiens
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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

View Full Validation Report



View more in-depth experimental data
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