9OX8 | pdb_00009ox8

NHEJ Short-range complex with Polymerase lambda

  • Classification: DNA BINDING PROTEIN/DNA
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens, Escherichia coli, unidentified baculovirus
  • Mutation(s): No 

  • Deposited: 2025-06-03 Released: 2026-07-01 
  • Deposition Author(s): Vogt, A., He, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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

Literature

End Processing in NHEJ by Polymerase lambda and PNKP is coordinated during short-range synapsis

Vogt, A., Kaminski, A.M., Pedersen, L.C., Naila, T., Tomkinson, A.E., Lees-Miller, S.P., Kunkel, T.A., He, Y.

To be published.

Macromolecule Content 

  • Total Structure Weight: 944.07 kDa 
  • Atom Count: 39,673 
  • Modeled Residue Count: 4,768 
  • Deposited Residue Count: 8,122 
  • Unique protein chains: 7
  • Unique nucleic acid chains: 2

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA ligase 4A,
T [auth X]		911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49917 (Homo sapiens)
Explore P49917 
Go to UniProtKB:  P49917
PHAROS:  P49917
GTEx:  ENSG00000174405 
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UniProt GroupP49917
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1
B, I
299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1, XLF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q4 (Homo sapiens)
Explore Q9H9Q4 
Go to UniProtKB:  Q9H9Q4
PHAROS:  Q9H9Q4
GTEx:  ENSG00000187736 
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UniProt GroupQ9H9Q4
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6
C, J
600Homo sapiensMutation(s): 0 
Gene Names: XRCC6, G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data), 5.6.2.4 (UniProt), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P12956 (Homo sapiens)
Explore P12956 
Go to UniProtKB:  P12956
PHAROS:  P12956
GTEx:  ENSG00000196419 
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UniProt GroupP12956
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5
D, K
732Homo sapiensMutation(s): 0 
EC: 5.6.2.4 (UniProt), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P13010 (Homo sapiens)
Explore P13010 
Go to UniProtKB:  P13010
PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase lambda
E, F
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
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4
G, H, O, P
336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13426 (Homo sapiens)
Explore Q13426 
Go to UniProtKB:  Q13426
PHAROS:  Q13426
GTEx:  ENSG00000152422 
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UniProt GroupQ13426
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein PAXXR [auth T],
S [auth U]		204Homo sapiensMutation(s): 0 
Gene Names: PAXX, C9orf142, XLS
UniProt
Find proteins for Q9BUH6 (Homo sapiens)
Explore Q9BUH6 
Go to UniProtKB:  Q9BUH6
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UniProt GroupQ9BUH6
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (34-MER)
L, N
34Homo sapiens
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Reference Sequence
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (34-MER)
M, Q
34Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6.2

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM135651
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM144559
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM008382
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01CA092584
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIC ES102645
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01 ES065070
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR24GM154185

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release