7LT3

NHEJ Long-range synaptic complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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,
K [auth J]		609Homo sapiensMutation(s): 0 
Gene Names: XRCC6, G22P1
EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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UniProt GroupP12956
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5B,
L [auth K]		732Homo sapiensMutation(s): 0 
Gene Names: XRCC5, G22P2
EC: 3.6.4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunitC,
M [auth L]		4,128Homo sapiensMutation(s): 0 
Gene Names: PRKDC, HYRC, HYRC1
EC: 2.7.11.1
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UniProt GroupP78527
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown peptideD [auth Q],
N [auth R]		20Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence 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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UniProt GroupQ13426
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1I [auth H],
J [auth I]		299Homo sapiensMutation(s): 0 
Gene Names: NHEJ1, XLF
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Entity ID: 9
MoleculeChainsSequence 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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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (31-MER)E [auth D],
O [auth M]		31Homo sapiens
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (30-MER)F [auth E],
P [auth N]		30Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP
Download Ideal Coordinates CCD File 
U [auth C],
V [auth L]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
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