5LUQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.437 
  • R-Value Work: 0.386 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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: 10.1126/science.aak9654

  • 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 th ...

    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.,Department of Biochemistry, University of Cambridge, Old Addenbrooke's Site, 80 Tennis Court Road, Cambridge CB2 1GA, UK. tlb20@cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit
A, B
4128Homo sapiensMutation(s): 0 
Gene Names: PRKDC (HYRC, HYRC1)
EC: 2.7.11.1
Find proteins for P78527 (Homo sapiens)
Go to Gene View: PRKDC
Go to UniProtKB:  P78527
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-terminal fragment of KU80 (KU80ct194)
K, S
194N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, K, S
L-PEPTIDE LINKINGC4 H9 N O2

--

MSE
Query on MSE
A, B, K, S
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.437 
  • R-Value Work: 0.386 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 169.120α = 90.00
b = 132.640β = 105.53
c = 296.590γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Source and taxonomy