7LSY

NHEJ Short-range synaptic complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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

    Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA. yuanhe@northwestern.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6A, I [auth J]600Homo 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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5B, J [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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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein XRCC4E [auth F], F [auth G], M [auth O], N [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
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1G [auth H], H [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
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase 4P [auth X], Q [auth Y]911Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (26-MER)C [auth D]26Homo sapiens
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3')D [auth E]14Homo sapiens
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    • Entity ID: 7
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3')K [auth M]14Homo sapiens
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      Entity ID: 8
      MoleculeChainsLengthOrganismImage
      DNA (26-MER)L [auth N]26Homo sapiens
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      • Entity ID: 9
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3')O [auth V]20Homo sapiens
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        Experimental Data & Validation

        Experimental Data

        • Method: ELECTRON MICROSCOPY
        • Resolution: 8.40 Å
        • Aggregation State: PARTICLE 
        • Reconstruction Method: SINGLE PARTICLE 

        Structure Validation

        View Full Validation Report




        Entry History & Funding Information

        Deposition Data

        • Deposited Date: 2021-02-18 
        • Released Date: 2021-04-14 
        • Deposition Author(s): He, Y., Chen, S.

        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
        American Cancer SocietyUnited StatesIRG-15-173-2
        National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01CA092584
        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