5LUQ

Crystal Structure of Human DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.437 
  • R-Value Work: 0.386 
  • R-Value Observed: 0.387 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7K17


Literature

DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair.

Sibanda, B.L.Chirgadze, D.Y.Ascher, D.B.Blundell, T.L.

(2017) Science 355: 520-524

  • DOI: https://doi.org/10.1126/science.aak9654
  • Primary Citation of Related Structures:  
    5LUQ

  • PubMed Abstract: 

    DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a central component of nonhomologous end joining (NHEJ), repairing DNA double-strand breaks that would otherwise lead to apoptosis or cancer. We have solved its structure in complex with the C-terminal peptide of Ku80 at 4.3 angstrom resolution using x-ray crystallography. We show that the 4128-amino acid structure comprises three large structural units: the N-terminal unit, the Circular Cradle, and the Head. Conformational differences between the two molecules in the asymmetric unit are correlated with changes in accessibility of the kinase active site, which are consistent with an allosteric mechanism to bring about kinase activation. The location of KU80ct 194 in the vicinity of the breast cancer 1 (BRCA1) binding site suggests competition with BRCA1, leading to pathway selection between NHEJ and homologous recombination.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Old Addenbrooke's Site, 80 Tennis Court Road, Cambridge CB2 1GA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunitA,
C [auth B]
4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78527 (Homo sapiens)
Explore P78527 
Go to UniProtKB:  P78527
PHAROS:  P78527
GTEx:  ENSG00000253729 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78527
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-terminal fragment of KU80 (KU80ct194)B [auth K],
D [auth S]
194Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
C [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.437 
  • R-Value Work: 0.386 
  • R-Value Observed: 0.387 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.12α = 90
b = 132.64β = 105.53
c = 296.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom093167/Z/10/Z

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Source and taxonomy
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary