7NFC

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 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: 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 ...

    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-PKcsA,
D [auth F]		4,148Homo sapiensMutation(s): 0 
Gene Names: PRKDC
EC: 2.7.11.1
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PHAROS:  P78527
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UniProt GroupP78527
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6B,
E [auth G]		609Homo sapiensMutation(s): 0 
Gene Names: XRCC6, G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5C,
F [auth H]		732Homo sapiensMutation(s): 0 
Gene Names: XRCC5, G22P2
EC: 3.6.4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein XRCC4G [auth K],
H [auth L],
J [auth N],
K [auth O]		336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase 4I [auth M],
L [auth P]		911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1M [auth Q],
N [auth R]		299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1, XLF
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Find proteins for Q9H9Q4 (Homo sapiens)
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (27-MER)O [auth D]27Homo sapiens
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (28-MER)P [auth E],
Q [auth I]		28Homo sapiens
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Entity ID: 9
MoleculeChainsLengthOrganismImage
DNA (27-MER)R [auth J]27Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 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 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