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TitleCryo-EM structures reveal the acetylation process of piccolo NuA4.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 12, Page e2414490122, Year 2025
Publish dateMar 25, 2025
AuthorsLin Wang / Haonan Zhang / Qi Jia / Wenyan Li / Chenguang Yang / Lijuan Ma / Ming Li / Ying Lu / Hongtao Zhu / Ping Zhu /
PubMed AbstractNuA4 is the only essential acetyltransferase in yeast that can catalyze the acetylation of the histones H2A, H2A.Z, and H4, thereby affecting gene transcription. However, the acetylation process of ...NuA4 is the only essential acetyltransferase in yeast that can catalyze the acetylation of the histones H2A, H2A.Z, and H4, thereby affecting gene transcription. However, the acetylation process of NuA4, such as how NuA4 acetylates H4 and H2A.Z differently, remains largely elusive. Here, using cryoelectron microscopy (cryo-EM) single particle analysis, we present seven cryo-EM structures of piccolo NuA4 (pNuA4) in complex with wild-type H2A.Z or H2A.Z-mutant-containing nucleosomes in the absence or presence of acetyl coenzyme A (Ac-CoA). We revealed that, in the absence of Ac-CoA, pNuA4 adopts multiple conformations to search for its substrates. After adding Ac-CoA, the single-molecule Förster resonance energy transfer (smFRET) and cryo-EM data indicated that pNuA4 prefers to bind H4 and undergoes a dynamic conformational change to complete the acetylation. We also obtained previously unseen structures in states associated with the acetylation of H2A.Z. These cryo-EM structures and smFRET results suggest a complex acetylation process on H4 and H2A.Z by pNuA4. The results provide a comprehensive picture of the mechanism by which pNuA4 acetylates its substrates within an H2A.Z-containing nucleosome.
External linksProc Natl Acad Sci U S A / PubMed:40100634 / PubMed Central
MethodsEM (single particle)
Resolution3.8 - 7.7 Å
Structure data

38021

8x2x

EMDB-38021, PDB-8x2x:
The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state
Method: EM (single particle) / Resolution: 3.8 Å

38022

8x2y

EMDB-38022, PDB-8x2y:
The class1 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
Method: EM (single particle) / Resolution: 4.1 Å

38023

8x2z

EMDB-38023, PDB-8x2z:
The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
Method: EM (single particle) / Resolution: 3.9 Å

38024

8x30

EMDB-38024, PDB-8x30:
Structure of piccolo NuA4 and H2A.Z nucleosome 2:1 complex
Method: EM (single particle) / Resolution: 4.3 Å

38025

8x31

EMDB-38025, PDB-8x31:
The piccolo NuA4 bound to the H2A.Z nucleosome complex with Ac-CoA at resetting state
Method: EM (single particle) / Resolution: 6.2 Å

38026

8x32

EMDB-38026, PDB-8x32:
The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ Complex with Ac-CoA at resetting state
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-60587: The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex without Ac-CoA at pre-H2A.Z-acetylation state
Method: EM (single particle) / Resolution: 7.7 Å

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • escherichia coli (E. coli)
  • schistosoma japonicum (invertebrata)
KeywordsGENE REGULATION / Nua4 / nucleosome

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