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 1.1 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

  • DOI: 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 ...

    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: tlb20@cam.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunitA4156Homo sapiensMutation(s): 0 
Gene Names: PRKDC
EC: 2.7.11.1
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Find proteins for P78527 (Homo sapiens)
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PHAROS:  P78527
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6B609Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5C732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
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Find proteins for P13010 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence 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
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein XRCC4F [auth H], G [auth I]336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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Find proteins for Q13426 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase 4H [auth J]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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Entity ID: 7
MoleculeChainsLengthOrganismImage
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
MoleculeChainsLengthOrganismImage
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 

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