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Structure paper

TitleStructural basis of long-range to short-range synaptic transition in NHEJ.
Journal, issue, pagesNature, Vol. 593, Issue 7858, Page 294-298, Year 2021
Publish dateApr 14, 2021
AuthorsSiyu Chen / Linda Lee / Tasmin Naila / Susan Fishbain / Annie Wang / Alan E Tomkinson / Susan P Lees-Miller / Yuan He /
PubMed AbstractDNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. The conserved error-prone non-homologous end joining (NHEJ) ...DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. 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. 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.
External linksNature / PubMed:33854234 / PubMed Central
MethodsEM (single particle)
Resolution4.1 - 9.3 Å
Structure data

23509

7lsy

EMDB-23509, PDB-7lsy:
NHEJ Short-range synaptic complex
Method: EM (single particle) / Resolution: 8.4 Å

23510

7lt3

EMDB-23510, PDB-7lt3:
NHEJ Long-range synaptic complex
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-23511:
DNA-PKcs, Ku, DNA and LigIV N-BRCT in the NHEJ Long-range synaptic complex
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-23512:
XLF, XRCC4 and LigIV C-BRCT in the NHEJ Long-range synaptic complex
Method: EM (single particle) / Resolution: 9.3 Å

EMDB-23513:
LigIV catalytic domain and distal Ku in the NHEJ Short-range synaptic complex
Method: EM (single particle) / Resolution: 6.8 Å

EMDB-23514:
Proximal Ku in NHEJ Short-range synaptic complex
Method: EM (single particle) / Resolution: 6.9 Å

EMDB-23515:
XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
Method: EM (single particle) / Resolution: 7.8 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
KeywordsDNA BINDING PROTEIN/DNA / NHEJ / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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