8EZA

NHEJ Long-range complex with PAXX


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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
Protein PAXXA [auth S],
S [auth T]
204Homo sapiensMutation(s): 0 
Gene Names: PAXXC9orf142XLS
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GTEx:  ENSG00000148362 
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UniProt GroupQ9BUH6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6B [auth J],
C [auth A]
609Homo sapiensMutation(s): 0 
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Find proteins for P12956 (Homo sapiens)
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PHAROS:  P12956
GTEx:  ENSG00000196419 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5D [auth K],
K [auth B]
732Homo sapiensMutation(s): 0 
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PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunitE [auth L],
L [auth C]
4,128Homo sapiensMutation(s): 0 
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Find proteins for P78527 (Homo sapiens)
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PHAROS:  P78527
GTEx:  ENSG00000253729 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit -- Unknown regionF [auth R],
M [auth Q]
20Homo sapiensMutation(s): 0 
EC: 2.7.11.1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1I [auth H],
J [auth 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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4P [auth F],
R [auth G],
T [auth O],
V [auth P]
336Homo sapiensMutation(s): 0 
Gene Names: XRCC4
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Find proteins for Q13426 (Homo sapiens)
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PHAROS:  Q13426
GTEx:  ENSG00000152422 
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UniProt GroupQ13426
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4Q [auth X],
U [auth Y]
911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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PHAROS:  P49917
GTEx:  ENSG00000174405 
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (31-MER)G [auth M],
N [auth D]
31Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (30-MER)H [auth N],
O [auth E]
30Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.39 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 StatesR01 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