8BOT

Cryo-EM structure of NHEJ supercomplex(trimer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ.

Hardwick, S.W.Stavridi, A.K.Chirgadze, D.Y.De Oliveira, T.M.Charbonnier, J.B.Ropars, V.Meek, K.Blundell, T.L.Chaplin, A.K.

(2023) Structure 31: 895

  • DOI: https://doi.org/10.1016/j.str.2023.05.013
  • Primary Citation of Related Structures:  
    8BOT

  • PubMed Abstract: 

    The ability of humans to maintain the integrity of the genome is imperative for cellular survival. DNA double-strand breaks (DSBs) are considered the most critical type of DNA lesion, which can ultimately lead to diseases including cancer. Non-homologous end joining (NHEJ) is one of two core mechanisms utilized to repair DSBs. DNA-PK is a key component in this process and has recently been shown to form alternate long-range synaptic dimers. This has led to the proposal that these complexes can be formed before transitioning to a short-range synaptic complex. Here we present cryo-EM data representing an NHEJ supercomplex consisting of a trimer of DNA-PK in complex with XLF, XRCC4, and DNA Ligase IV. This trimer represents a complex of both long-range synaptic dimers. We discuss the potential role of the trimeric structure, and possible higher order oligomers, as structural intermediates in the NHEJ mechanism, or as functional DNA repair centers.


  • Organizational Affiliation

    Cryo-EM Facility, Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, CB2 1GA Cambridge, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4A [auth K],
B [auth L],
D [auth N],
E [auth O]
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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4C [auth M],
F [auth P]
911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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GTEx:  ENSG00000174405 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1G [auth Q],
H [auth R],
X,
Y
299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1XLF
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Find proteins for Q9H9Q4 (Homo sapiens)
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GTEx:  ENSG00000187736 
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UniProt GroupQ9H9Q4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunitI [auth F],
N [auth A],
S
4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
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GTEx:  ENSG00000253729 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6J [auth G],
O [auth B],
T
609Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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GTEx:  ENSG00000196419 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5K [auth H],
P [auth C],
U
732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
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GTEx:  ENSG00000079246 
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (28-MER)L [auth I],
V
28Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (27-MER)M [auth J],
W
27Homo sapiens
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (24-MER)Q [auth D]24Homo sapiens
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (24-MER)R [auth E]24Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.76 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
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references