7NFE

Cryo-EM structure of NHEJ super-complex (monomer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.

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

(2021) Mol Cell 81: 3400-3409

  • DOI: https://doi.org/10.1016/j.molcel.2021.07.005
  • Primary Citation of Related Structures:  
    7NFC, 7NFE

  • PubMed Abstract: 

    Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or cancer. NHEJ involves several proteins, including the Ku70/80 heterodimer, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and ligase IV. These core proteins bind DSBs and ligate the damaged DNA ends. However, details of the structural assembly of these proteins remain unclear. Here, we present cryo-EM structures of NHEJ supercomplexes that are composed of these core proteins and DNA, revealing the detailed structural architecture of this assembly. We describe monomeric and dimeric forms of this supercomplex and also propose the existence of alternate dimeric forms of long-range synaptic complexes. Finally, we show that mutational disruption of several structural features within these NHEJ complexes negatively affects DNA repair.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address: ac821@cam.ac.uk.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit4,156Homo 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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UniProt GroupP78527
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6609Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
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PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1D [auth F],
E [auth G]
299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1XLF
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Find proteins for Q9H9Q4 (Homo sapiens)
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PHAROS:  Q9H9Q4
GTEx:  ENSG00000187736 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4F [auth H],
G [auth I]
336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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GTEx:  ENSG00000152422 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4H [auth J]911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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PHAROS:  P49917
GTEx:  ENSG00000174405 
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  • Reference Sequence

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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*AP*TP*AP*AP*AP*CP*TP*AP*AP*AP*AP*AP*CP*TP*AP*TP*TP*AP*TP*TP*AP*TP*G)-3')I [auth D]24Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*AP*TP*AP*AP*TP*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*AP*G)-3')J [auth E]24Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200814/Z/16/Z; 2016

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Database references