7SGL

DNA-PK complex of DNA end processing

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Autophosphorylation transforms DNA-PK from protecting to processing DNA ends.

Liu, L., Chen, X., Li, J., Wang, H., Buehl, C.J., Goff, N.J., Meek, K., Yang, W., Gellert, M.

(2022) Mol Cell 82: 177

  • DOI: 10.1016/j.molcel.2021.11.025
  • Primary Citation of Related Structures:  
    7SGL, 7SU3, 7SUD

  • PubMed Abstract: 

    • The DNA-dependent protein kinase (DNA-PK) initially protects broken DNA ends but then promotes their processing during non-homologous end joining (NHEJ). Before ligation by NHEJ, DNA hairpin ends generated during V(D)J recombination must be opened by the Artemis nuclease, together with autophosphorylated DNA-PK ...

    The DNA-dependent protein kinase (DNA-PK) initially protects broken DNA ends but then promotes their processing during non-homologous end joining (NHEJ). Before ligation by NHEJ, DNA hairpin ends generated during V(D)J recombination must be opened by the Artemis nuclease, together with autophosphorylated DNA-PK. Structures of DNA-PK bound to DNA before and after phosphorylation, and in complex with Artemis and a DNA hairpin, reveal an essential functional switch. When bound to open DNA ends in its protection mode, DNA-PK is inhibited for cis-autophosphorylation of the so-called ABCDE cluster but activated for phosphorylation of other targets. In contrast, DNA hairpin ends promote cis-autophosphorylation. Phosphorylation of four Thr residues in ABCDE leads to gross structural rearrangement of DNA-PK, widening the DNA binding groove for Artemis recruitment and hairpin cleavage. Meanwhile, Artemis locks DNA-PK into the kinase-inactive state. Kinase activity and autophosphorylation of DNA-PK are regulated by different DNA ends, feeding forward to coordinate NHEJ events.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: martinge@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
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Find proteins for P78527 (Homo sapiens)
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PHAROS:  P78527
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UniProt GroupP78527
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6B612Homo 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)
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PHAROS:  P12956
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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)
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PHAROS:  P13010
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UniProt GroupP13010
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein artemisD701Homo sapiensMutation(s): 0 
Gene Names: DCLRE1C, ARTEMIS, ASCID, SCIDA, SNM1C
EC: 3.1
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Find proteins for Q96SD1 (Homo sapiens)
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PHAROS:  Q96SD1
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UniProt GroupQ96SD1
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Hairpin_1E, F54synthetic construct
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 StatesM.G., DK036167
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesW.Y., DK036147
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK036144

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references