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Structure paper

TitleMolecular basis of nick ligation in the nucleosome by DNA Ligase III alpha
Journal, issue, pagesNat Commun, Year 2026
Publish dateFeb 12, 2026 (structure data deposition date)
AuthorsBoesch DJ / Martin NI / Kontor CA / Nguyen AG / Tomkinson AE / Van Houten B / Gillet N / Bignon E / Whitaker AM / Weaver TM
External linksNat Commun / Search PubMed
MethodsEM (single particle)
Resolution2.5 - 3.9 Å
Structure data

75521

10xz

EMDB-75521, PDB-10xz:
Non-damaged nucleosome
Method: EM (single particle) / Resolution: 2.6 Å

75522

10ya

EMDB-75522, PDB-10ya:
Nucleosome containing a nick at SHL0
Method: EM (single particle) / Resolution: 2.7 Å

75523

10yb

EMDB-75523, PDB-10yb:
Nucleosome containing a nick at SHL-2
Method: EM (single particle) / Resolution: 2.8 Å

75524

10yc

EMDB-75524, PDB-10yc:
Nucleosome containing a nick at SHL-4
Method: EM (single particle) / Resolution: 2.7 Å

75525

10yd

EMDB-75525, PDB-10yd:
Nucleosome containing a nick at SHL-6
Method: EM (single particle) / Resolution: 2.8 Å

75526

10ye

EMDB-75526, PDB-10ye:
DNA Ligase IIIa bound to nucleosome containing a nick at SHL0
Method: EM (single particle) / Resolution: 2.5 Å

75527

10yf

EMDB-75527, PDB-10yf:
DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite)
Method: EM (single particle) / Resolution: 3.0 Å

75528

10yg

EMDB-75528, PDB-10yg:
DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite)
Method: EM (single particle) / Resolution: 3.4 Å

75529

10yh

EMDB-75529, PDB-10yh:
DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite)
Method: EM (single particle) / Resolution: 2.9 Å

75530

10yi

EMDB-75530, PDB-10yi:
XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-75531: DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (consensus)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-75532: DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (LigIIIa/DNA local refine)
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-75533: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (consensus)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-75534: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (LigIIIa/DNA local refine)
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-75535: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (consensus)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-75536: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (LigIIIa/DNA local refine)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-75537: XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (consensus)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-75538: XRCC1-DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (LigIIIa/DNA local refine)
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN/DNA / Nucleosome / DNA Ligase IIIa / DNA Repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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