5LUQ | pdb_00005luq

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

• PDB DOI: https://doi.org/10.2210/pdb5LUQ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-09 Released: 2017-02-15 
• Deposition Author(s): Sibanda, B.L., Chirgadze, D.Y., Ascher, D.B., Blundell, T.L.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.30 Å
• R-Value Free: 
  0.437 (Depositor), 0.444 (DCC) 
• R-Value Work: 
  0.386 (Depositor), 0.388 (DCC) 
• R-Value Observed: 
  0.387 (Depositor) 

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

• PubMed: 28154079 
• DOI: https://doi.org/10.1126/science.aak9654
• Primary Citation 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.

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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. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 972.48 kDa 
• Atom Count: 59,694 
• Modeled Residue Count: 7,558 
• Deposited Residue Count: 8,644 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit	A, C [auth B]	4,128	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal fragment of KU80 (KU80ct194)	B [auth K], D [auth S]	194	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C [auth B]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
UNK	A, C [auth B]	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.30 Å
• R-Value Free:  0.437 (Depositor), 0.444 (DCC) 
• R-Value Work:  0.386 (Depositor), 0.388 (DCC) 
• R-Value Observed: 0.387 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.12	α = 90
b = 132.64	β = 105.53
c = 296.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Sibanda, B.L., Chirgadze, D.Y., Ascher, D.B., Blundell, T.L.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	093167/Z/10/Z

Revision History  

• 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