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TitleMechanistic insights into histone recognition and H3K14 acetylation by the NuA3 histone acetyltransferase complex.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Page 342, Year 2025
Publish dateNov 29, 2025
AuthorsWenping Shi / Lixia Zhao / Yiru Wang / Yi Zhang / Simiao Liu / Yannan Wang / Roger D Kornberg / Heqiao Zhang /
PubMed AbstractThe NuA3 histone acetyltransferase complex in budding yeast, composed of six subunits, specifically acetylates lysine 14 on histone H3 (H3K14), thereby regulating various biological processes. ...The NuA3 histone acetyltransferase complex in budding yeast, composed of six subunits, specifically acetylates lysine 14 on histone H3 (H3K14), thereby regulating various biological processes. Despite its importance, the structural basis and mechanism underlying histone tail recognition and substrate specificity of the NuA3 complex have remained elusive. Here we report cryo-electron microscopy structures of the NuA3 complex in its apo form, bound to acetyl-coenzyme A (acetyl-CoA), and in a complex with both the histone H3 tail and acetyl-CoA. Our structure shows that the histone tail-binding cleft of NuA3 is formed cooperatively by two subunits, the catalytic subunit Sas3 and the non-catalytic subunit Nto1. A hydrophobic part of the cleft engages the region preceding H3K14 (residues 9-12), while a network of polar interactions between the cleft and the backbone of H3 residues 12-15, particularly involving Gly13, contributes to substrate specificity.
External linksNat Commun / PubMed:41318527 / PubMed Central
MethodsEM (single particle)
Resolution3.13 - 3.68 Å
Structure data

64513

9uuo

EMDB-64513, PDB-9uuo:
The NuA3 histone acetyltransferase complex
Method: EM (single particle) / Resolution: 3.68 Å

64517

9uus

EMDB-64517, PDB-9uus:
The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail
Method: EM (single particle) / Resolution: 3.2 Å

65145

9vkw

EMDB-65145, PDB-9vkw:
Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A
Method: EM (single particle) / Resolution: 3.13 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-ACO:
ACETYL COENZYME *A

Source
  • Saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsMETAL BINDING PROTEIN / DNA / nucleosome / histone acetylation / TRANSFERASE / NuA3 / Cryo-EM / Histone

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