9UUS | pdb_00009uus

The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Mechanistic insights into histone recognition and H3K14 acetylation by the NuA3 histone acetyltransferase complex.

Shi, W.Zhao, L.Wang, Y.Zhang, Y.Liu, S.Wang, Y.Kornberg, R.D.Zhang, H.

(2025) Nat Commun 17: 342-342

  • DOI: https://doi.org/10.1038/s41467-025-67049-0
  • Primary Citation Related Structures: 
    9UUO, 9UUS, 9VKW

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 252.01 kDa 
  • Atom Count: 10,835 
  • Modeled Residue Count: 1,313 
  • Deposited Residue Count: 2,166 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3A [auth H]21Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHT1YBR010WYBR0201HHT2SIN2YNL031CN2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P61830
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UniProt GroupP61830
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone acetyltransferase SAS3B [auth A]831Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS3YBL052CYBL0507YBL0515
EC: 2.3.1.48
UniProt
Find proteins for P34218 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34218 
Go to UniProtKB:  P34218
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UniProt GroupP34218
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NuA3 HAT complex component NTO1C [auth B]738Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NTO1YPR031W
UniProt
Find proteins for Q12311 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12311
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UniProt GroupQ12311
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein YNG1D [auth C]219Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YNG1YOR064CYOR29-15
UniProt
Find proteins for Q08465 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ08465
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 14244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TAF14ANC1CST10SWP29TAF30TFG3YPL129W
UniProt
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP35189
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF6F [auth D]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EAF6YJR082CJ1854
UniProt
Find proteins for P47128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P47128
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UniProt GroupP47128
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1_3660
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Data collection, Database references