9N81 | pdb_00009n81

A gap-filling complex with Pol mu engaged in the NHEJ Pathway


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Dynamic assemblies and coordinated reactions of non-homologous end joining.

Liu, L.Li, J.Cisneros-Aguirre, M.Merkell, A.Stark, J.M.Gellert, M.Yang, W.

(2025) Nature 643: 847-854

  • DOI: https://doi.org/10.1038/s41586-025-09078-9
  • Primary Citation of Related Structures:  
    9CQ3, 9CQ6, 9CQC, 9N81, 9N82, 9N83

  • PubMed Abstract: 

    Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes 1,2 . Here we report reconstitution of the final steps of NHEJ and structures of DNA polymerase μ and ligase IV (LIG4) engaged in gap filling and end joining. These reactions take place in a flexible ω-shaped framework composed of XRCC4 and XLF. Two broken DNA ends, each encircled by Ku70-Ku80 internally, are docked onto the ω frame, mediated by LIG4. DNA polymerase and ligase attached to each ω arm repair only one broken strand of a defined polarity; the final steps of NHEJ requires coordination and toggling of a pair of such enzymes. The facilitators XLF and PAXX additively stimulate NHEJ reactions. As DNA-end sensor and protector, LIG4 replaces DNA-PKcs for end joining and bridges the two DNA ends for polymerase to fill remaining gaps. These assemblies present new targets for NHEJ inhibition to enhance efficacy of radiotherapy and accuracy of gene editing.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6A,
N [auth a]
612Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5B,
O [auth b]
732Homo sapiensMutation(s): 0 
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
Non-homologous end-joining factor 1C,
P [auth c]
302Homo sapiensMutation(s): 0 
Gene Names: NHEJ1XLF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q4 (Homo sapiens)
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Go to UniProtKB:  Q9H9Q4
PHAROS:  Q9H9Q4
GTEx:  ENSG00000187736 
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UniProt GroupQ9H9Q4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4D,
E,
Q [auth d],
R [auth e]
336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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GTEx:  ENSG00000152422 
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UniProt GroupQ13426
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4F,
S [auth f]
914Homo 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PAXX
G, H
218Homo sapiensMutation(s): 0 
Gene Names: PAXXC9orf142XLS
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GTEx:  ENSG00000148362 
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UniProt GroupQ9BUH6
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed DNA/RNA polymerase muM,
T [auth m]
512Homo sapiensMutation(s): 0 
Gene Names: POLMpolmu
EC: 2.7.7.7
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Find proteins for Q9NP87 (Homo sapiens)
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PHAROS:  Q9NP87
GTEx:  ENSG00000122678 
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UniProt GroupQ9NP87
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (38-MER)68Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (42-MER)68Homo sapiens
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (34-MER)51Homo sapiens
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (37-MER)50Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DZ4
Query on DZ4

Download Ideal Coordinates CCD File 
V [auth M]2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
C10 H17 N6 O11 P3
WKIPJDSLGCBQCU-RRKCRQDMSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
U [auth M]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-25
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-30
    Changes: Data collection, Database references