5Y3R

Cryo-EM structure of Human DNA-PK Holoenzyme

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

  • Deposited: 2017-07-29 Released: 2017-09-06 
  • Deposition Author(s): Yin, X., Liu, M., Tian, Y., Wang, J., Xu, Y.
  • Funding Organization(s): Ministry of Science and Technology of China; Strategic Priority Research Program of the Chinese Academy of Sciences; National Natural Science Foundation of China; Program of Shanghai Subject Chief Scientist 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of human DNA-PK holoenzyme

Yin, X.Liu, M.Tian, Y.Wang, J.Xu, Y.

(2017) Cell Res. 27: 1341-1350

  • DOI: 10.1038/cr.2017.110

  • PubMed Abstract: 
  • DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the majo ...

    DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the major DNA repair pathway. Here, we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6 Å resolution. In the complex structure, DNA-PKcs, KU70, KU80 and DNA duplex form a 650-kDa heterotetramer with 1:1:1:1 stoichiometry. The N-terminal α-solenoid (∼2 800 residues) of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/80-DNA. DNA-PKcs and KU70/80 together form a DNA-binding tunnel, which cradles ∼30-bp DNA and prevents sliding inward of DNA-PKcs along with DNA duplex, suggesting a mechanism by which the broken DNA end is protected from unnecessary processing. Structural and biochemical analyses indicate that KU70/80 and DNA coordinately induce conformational changes of DNA-PKcs and allosterically stimulate its kinase activity. We propose a model for activation of DNA-PKcs in which allosteric signals are generated upon DNA-PK holoenzyme formation and transmitted to the kinase domain through N-terminal HEAT repeats and FAT domain of DNA-PKcs. Our studies suggest a mechanism for recognition and protection of broken DNA ends and provide a structural basis for understanding the activation of DNA-PKcs and DNA-PK-mediated NHEJ pathway.


    Organizational Affiliation

    Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.,Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
X-ray repair cross-complementing protein 6
A
501Homo sapiensMutation(s): 0 
Gene Names: XRCC6 (G22P1)
EC: 3.6.4.-, 4.2.99.-
Find proteins for P12956 (Homo sapiens)
Go to Gene View: XRCC6
Go to UniProtKB:  P12956
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
X-ray repair cross-complementing protein 5
B
536Homo sapiensMutation(s): 0 
Gene Names: XRCC5 (G22P2)
EC: 3.6.4.-
Find proteins for P13010 (Homo sapiens)
Go to Gene View: XRCC5
Go to UniProtKB:  P13010
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PRKDC-Helix
K
15N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-dependent protein kinase catalytic subunit
C
4119Homo 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: 4
MoleculeChainsLengthOrganism
DNA (34-MER)D34Homo sapiens
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (36-MER)E36Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.6 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
Ministry of Science and Technology of ChinaChina2016YFA0500700
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08000000
National Natural Science Foundation of ChinaChinaU1432242,31425008,91419301
Program of Shanghai Subject Chief ScientistChina14XD1400500

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Source and taxonomy