5W1R

Cryo-EM structure of DNAPKcs

  • Classification: DNA BINDING PROTEIN
  • Organism(s): Homo sapiens

  • Deposited: 2017-06-04 Released: 2017-07-19 
  • Deposition Author(s): Sharif, H., Li, Y., Wu, H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of the DNA-PK holoenzyme.

Sharif, H.Li, Y.Dong, Y.Dong, L.Wang, W.L.Mao, Y.Wu, H.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 7367-7372

  • DOI: 10.1073/pnas.1707386114

  • PubMed Abstract: 
  • DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, ...

    DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, we report the cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs at 4.4-Å resolution and the DNA-PK holoenzyme at 5.8-Å resolution. The DNA-PKcs structure contains three distinct segments: the N-terminal region with an arm and a bridge, the circular cradle, and the head that includes the kinase domain. Two perpendicular apertures exist in the structure, which are sufficiently large for the passage of dsDNA. The DNA-PK holoenzyme cryo-EM map reveals density for the C-terminal globular domain of Ku80 that interacts with the arm of DNA-PKcs. The Ku80-binding site is adjacent to the previously identified density for the DNA-binding region of the Ku70/Ku80 complex, suggesting concerted DNA interaction by DNA-PKcs and the Ku complex.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-dependent protein kinase catalytic subunit
A
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI125535

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence