8EZB

NHEJ Long-range complex with ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 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 visualization of DNA-PKcs structural intermediates in NHEJ.

Chen, S.Vogt, A.Lee, L.Naila, T.McKeown, R.Tomkinson, A.E.Lees-Miller, S.P.He, Y.

(2023) Sci Adv 9: eadg2838-eadg2838

  • DOI: https://doi.org/10.1126/sciadv.adg2838
  • Primary Citation of Related Structures:  
    8EZ9, 8EZA, 8EZB

  • PubMed Abstract: 

    DNA double-strand breaks (DSBs), one of the most cytotoxic forms of DNA damage, can be repaired by the tightly regulated nonhomologous end joining (NHEJ) machinery (Stinson and Loparo and Zhao et al. ). Core NHEJ factors form an initial long-range (LR) synaptic complex that transitions into a DNA-PKcs (DNA-dependent protein kinase, catalytic subunit)-free, short-range state to align the DSB ends (Chen et al. ). Using single-particle cryo-electron microscopy, we have visualized three additional key NHEJ complexes representing different transition states, with DNA-PKcs adopting distinct dimeric conformations within each of them. Upon DNA-PKcs autophosphorylation, the LR complex undergoes a substantial conformational change, with both Ku and DNA-PKcs rotating outward to promote DNA break exposure and DNA-PKcs dissociation. We also captured a dimeric state of catalytically inactive DNA-PKcs, which resembles structures of other PIKK (Phosphatidylinositol 3-kinase-related kinase) family kinases, revealing a model of the full regulatory cycle of DNA-PKcs during NHEJ.


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6
A, J
609Homo sapiensMutation(s): 0 
Gene Names: XRCC6G22P1
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
GTEx:  ENSG00000196419 
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UniProt GroupP12956
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5
B, K
732Homo sapiensMutation(s): 0 
Gene Names: XRCC5G22P2
EC: 3.6.4
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Find proteins for P13010 (Homo sapiens)
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PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunit
C, L
4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
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Find proteins for P78527 (Homo sapiens)
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PHAROS:  P78527
GTEx:  ENSG00000253729 
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UniProt GroupP78527
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4
F, G, O, P
336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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Find proteins for Q13426 (Homo sapiens)
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GTEx:  ENSG00000152422 
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UniProt GroupQ13426
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1
H, I
299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1XLF
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Find proteins for Q9H9Q4 (Homo sapiens)
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PHAROS:  Q9H9Q4
GTEx:  ENSG00000187736 
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UniProt GroupQ9H9Q4
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PAXXQ [auth S],
R [auth T]
204Homo sapiensMutation(s): 0 
Gene Names: PAXXC9orf142XLS
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Find proteins for Q9BUH6 (Homo sapiens)
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GTEx:  ENSG00000148362 
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UniProt GroupQ9BUH6
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4S [auth X],
T [auth Y]
911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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Find proteins for P49917 (Homo sapiens)
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GTEx:  ENSG00000174405 
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (31-MER)
D, M
31Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (30-MER)
E, N
30Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE1.3
RECONSTRUCTIONRELION3.1.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM135651
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection