7K1N

CryoEM structure of inactivated-form DNA-PK (Complex V)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

Structure of an activated DNA-PK and its implications for NHEJ.

Chen, X., Xu, X., Chen, Y., Cheung, J.C., Wang, H., Jiang, J., de Val, N., Fox, T., Gellert, M., Yang, W.

(2021) Mol Cell 81: 801-810.e3

  • DOI: 10.1016/j.molcel.2020.12.015
  • Primary Citation of Related Structures:  
    7K0Y, 7K10, 7K11, 7K17, 7K19, 7K1B, 7K1J, 7K1K, 7K1N

  • PubMed Abstract: 

    • DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved ...

    DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved. For DNA-PK, all existing structures represent inactive states with resolution limited to 4.3 Å at best. Here, we report the cryoelectron microscopy (cryo-EM) structures of DNA-PKcs (DNA-PK catalytic subunit) bound to a DNA end or complexed with Ku70/80 and DNA in both inactive and activated forms at resolutions of 3.7 Å overall and 3.2 Å for FATKINs. These structures reveal the sequential transition of DNA-PK from inactive to activated forms. Most notably, activation of the kinase involves previously unknown stretching and twisting within individual solenoid segments and loosens DNA-end binding. This unprecedented structural plasticity of helical repeats may be a general regulatory mechanism of HEAT-repeat proteins.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: weiy@niddk.nih.gov.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunitA4,128Homo sapiensMutation(s): 0 
Gene Names: PRKDC, HYRC, HYRC1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78527 (Homo sapiens)
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Go to UniProtKB:  P78527
PHAROS:  P78527
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UniProt GroupP78527
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6B609Homo sapiensMutation(s): 0 
Gene Names: XRCC6, G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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Find proteins for P12956 (Homo sapiens)
Explore P12956 
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PHAROS:  P12956
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UniProt GroupP12956
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5C732Homo sapiensMutation(s): 0 
Gene Names: XRCC5, G22P2
EC: 3.6.4
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Find proteins for P13010 (Homo sapiens)
Explore P13010 
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PHAROS:  P13010
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UniProt GroupP13010
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')D, F24synthetic construct
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3')E, G16synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Structure summary
  • Version 1.3: 2021-03-03
    Changes: Database references