6ZHA

Cryo-EM structure of DNA-PK monomer

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.91 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

Dimers of DNA-PK create a stage for DNA double-strand break repair.

Chaplin, A.K., Hardwick, S.W., Liang, S., Kefala Stavridi, A., Hnizda, A., Cooper, L.R., De Oliveira, T.M., Chirgadze, D.Y., Blundell, T.L.

(2021) Nat Struct Mol Biol 28: 13-19

  • DOI: 10.1038/s41594-020-00517-x
  • Primary Citation of Related Structures:  
    6ZFP, 6ZH2, 6ZH4, 6ZH6, 6ZH8, 6ZHA, 6ZHE

  • PubMed Abstract: 

    • DNA double-strand breaks are the most dangerous type of DNA damage and, if not repaired correctly, can lead to cancer. In humans, Ku70/80 recognizes DNA broken ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form DNA-dependent protein kinase holoenzyme (DNA-PK) in the process of non-homologous end joining (NHEJ) ...

    DNA double-strand breaks are the most dangerous type of DNA damage and, if not repaired correctly, can lead to cancer. In humans, Ku70/80 recognizes DNA broken ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form DNA-dependent protein kinase holoenzyme (DNA-PK) in the process of non-homologous end joining (NHEJ). We present a 2.8-Å-resolution cryo-EM structure of DNA-PKcs, allowing precise amino acid sequence registration in regions uninterpreted in previous 4.3-Å X-ray maps. We also report a cryo-EM structure of DNA-PK at 3.5-Å resolution and reveal a dimer mediated by the Ku80 C terminus. Central to dimer formation is a domain swap of the conserved C-terminal helix of Ku80. Our results suggest a new mechanism for NHEJ utilizing a DNA-PK dimer to bring broken DNA ends together. Furthermore, drug inhibition of NHEJ in combination with chemo- and radiotherapy has proved successful, making these models central to structure-based drug targeting efforts.

    Related Citations: 
    • Dimers of DNA-PK create a stage for DNA-double strand break repair
      Chaplin, A.K., Hardwick, S.W., Liang, S., Stavridi, A.K., Hnizda, A., Cooper, L.R., De Oliveira, T.M., Chirgadze, D.Y., Blundell, T.L.
      (2020) Nat Struct Mol Biol --: --
    Organizational Affiliation: 

    Department of Biochemistry, University of Cambridge, Cambridge, UK. 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 subunit,DNA-PKcsA4,156Homo 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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UniProt GroupP78527
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6B609Homo sapiensMutation(s): 0 
Gene Names: XRCC6, G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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Find proteins for P12956 (Homo sapiens)
Explore P12956 
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PHAROS:  P12956
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UniProt GroupP12956
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5C732Homo sapiensMutation(s): 0 
Gene Names: XRCC5, G22P2
EC: 3.6.4
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Find proteins for P13010 (Homo sapiens)
Explore P13010 
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PHAROS:  P13010
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UniProt GroupP13010
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNAD25Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNAE24Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references