3KGV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.6 Å
  • R-Value Free: 0.441 
  • R-Value Work: 0.442 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats.

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

(2010) Nature 463: 118-121

  • DOI: 10.1038/nature08648

  • PubMed Abstract: 
  • Broken chromosomes arising from DNA double-strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation. Left unrepaired or inco ...

    Broken chromosomes arising from DNA double-strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holoenzyme that comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer Ku70/Ku80, has a major role in non-homologous end joining-the main pathway in mammals used to repair double-strand breaks. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids and belonging to the phosphatidylinositol-3-OH kinase (PI(3)K)-related protein family. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA. Here we present the crystal structure of human DNA-PKcs at 6.6 A resolution, in which the overall fold is clearly visible, to our knowledge, for the first time. The many alpha-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The carboxy-terminal kinase domain is located on top of this structure, and a small HEAT repeat domain that probably binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Old Addenbrooke's site, 80 Tennis Court Road, Cambridge CB2 1GA, UK. lynn@cryst.bioc.cam.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-dependent Protein Kinase Catalytic Subunit
A, B, C, D, E, F, X, O, P, Q, R, S, T, Y
4128N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, C, D, E, F, O, P, Q, R, S, T, X, Y
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.6 Å
  • R-Value Free: 0.441 
  • R-Value Work: 0.442 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 168.600α = 90.00
b = 132.990β = 105.58
c = 297.000γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXphasing
PHENIXmodel building
SCALEPACKdata scaling
MxCuBEdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-07-23
    Type: Other