7LT3

NHEJ Long-range synaptic complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of long-range to short-range synaptic transition in NHEJ.

Chen, S.Lee, L.Naila, T.Fishbain, S.Wang, A.Tomkinson, A.E.Lees-Miller, S.P.He, Y.

(2021) Nature 593: 294-298

  • DOI: https://doi.org/10.1038/s41586-021-03458-7
  • Primary Citation of Related Structures:  
    7LSY, 7LT3

  • PubMed Abstract: 

    DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis 1,2 . The conserved error-prone non-homologous end joining (NHEJ) pathway has a key role in determining the effects of DSB-inducing agents that are used to treat cancer as well as the generation of the diversity in antibodies and T cell receptors 2,3 . Here we applied single-particle cryo-electron microscopy to visualize two key DNA-protein complexes that are formed by human NHEJ factors. The Ku70/80 heterodimer (Ku), the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), DNA ligase IV (LigIV), XRCC4 and XLF form a long-range synaptic complex, in which the DNA ends are held approximately 115 Å apart. Two DNA end-bound subcomplexes comprising Ku and DNA-PKcs are linked by interactions between the DNA-PKcs subunits and a scaffold comprising LigIV, XRCC4, XLF, XRCC4 and LigIV. The relative orientation of the DNA-PKcs molecules suggests a mechanism for autophosphorylation in trans, which leads to the dissociation of DNA-PKcs and the transition into the short-range synaptic complex. Within this complex, the Ku-bound DNA ends are aligned for processing and ligation by the XLF-anchored scaffold, and a single catalytic domain of LigIV is stably associated with a nick between the two Ku molecules, which suggests that the joining of both strands of a DSB involves both LigIV molecules.


  • 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 6A,
K [auth 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 5B,
L [auth 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 subunitC,
M [auth L]
4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideD [auth Q],
N [auth R]
20Homo sapiensMutation(s): 0 
Sequence Annotations
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein XRCC4G [auth F],
H [auth G],
Q [auth O],
R [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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  • Reference Sequence
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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
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q4 (Homo sapiens)
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Go to UniProtKB:  Q9H9Q4
PHAROS:  Q9H9Q4
GTEx:  ENSG00000187736 
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UniProt GroupQ9H9Q4
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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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PHAROS:  P49917
GTEx:  ENSG00000174405 
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UniProt GroupP49917
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (31-MER)E [auth D],
O [auth M]
31Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (30-MER)F [auth E],
P [auth N]
30Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

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 StatesR01GM135651
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM008382
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01CA092584
American Cancer SocietyUnited StatesIRG-15-173-21
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM047251

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description