5Y3R

Cryo-EM structure of Human DNA-PK Holoenzyme

  • Classification: DNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • 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: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/cr.2017.110
  • Primary Citation of Related Structures:  
    5Y3R

  • 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6501Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12956 (Homo sapiens)
Explore P12956 
Go to UniProtKB:  P12956
PHAROS:  P12956
GTEx:  ENSG00000196419 
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UniProt GroupP12956
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5536Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P13010 (Homo sapiens)
Explore P13010 
Go to UniProtKB:  P13010
PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PRKDC-HelixC [auth K]15Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunitF [auth C]4,119Homo sapiensMutation(s): 0 
Gene Names: PRKDCHYRCHYRC1
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 
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UniProt GroupP78527
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (34-MER)34Homo sapiens
Sequence Annotations
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (36-MER)36Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2018-06-13
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2019-10-09
    Changes: Data collection, Other