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- PDB-9uus: The NuA3 histone acetyltransferase complex bound to acetyl-CoA an... -

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Basic information

Entry
Database: PDB / ID: 9uus
TitleThe NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail
Components
  • Chromatin modification-related protein EAF6
  • Histone H3
  • Histone acetyltransferase SAS3
  • NuA3 HAT complex component NTO1
  • Protein YNG1
  • Transcription initiation factor TFIID subunit 14
KeywordsMETAL BINDING PROTEIN / DNA / nucleosome / histone acetylation
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / histone H3K36me3 reader activity / Condensation of Prophase Chromosomes ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / histone H3K36me3 reader activity / Condensation of Prophase Chromosomes / : / : / Platelet degranulation / : / Assembly of the ORC complex at the origin of replication / SUMOylation of transcription cofactors / transcription factor TFIIF complex / mediator complex / Oxidative Stress Induced Senescence / Ino80 complex / histone H3K4me3 reader activity / silent mating-type cassette heterochromatin formation / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase activity / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / RNA Polymerase I Promoter Escape / rRNA transcription / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / intracellular copper ion homeostasis / subtelomeric heterochromatin formation / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / CENP-A containing nucleosome / aerobic respiration / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / DNA repair / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / ING family / YEATS / : / : / YEATS superfamily / YEATS family / YEATS domain profile. ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / ING family / YEATS / : / : / YEATS superfamily / YEATS family / YEATS domain profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Zinc finger, PHD-type, conserved site / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / Histone acetyltransferase SAS3 / Transcription initiation factor TFIID subunit 14 / Chromatin modification-related protein EAF6 / Histone H3 / Protein YNG1 / NuA3 HAT complex component NTO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, Y.R. / Zhang, H.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic insights into histone recognition and H3K14 acetylation by the NuA3 histone acetyltransferase complex.
Authors: Wenping Shi / Lixia Zhao / Yiru Wang / Yi Zhang / Simiao Liu / Yannan Wang / Roger D Kornberg / Heqiao Zhang /
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. ...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.
History
DepositionMay 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 2.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Histone H3
A: Histone acetyltransferase SAS3
B: NuA3 HAT complex component NTO1
C: Protein YNG1
E: Transcription initiation factor TFIID subunit 14
D: Chromatin modification-related protein EAF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,00612
Polymers250,8696
Non-polymers1,1376
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 1 types, 1 molecules H

#1: Protein/peptide Histone H3


Mass: 2263.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61830

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Protein , 5 types, 5 molecules ABCED

#2: Protein Histone acetyltransferase SAS3 / Something about silencing protein 3


Mass: 97723.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SAS3, YBL052C, YBL0507, YBL0515 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34218, histone acetyltransferase
#3: Protein NuA3 HAT complex component NTO1


Mass: 85102.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: NTO1, YPR031W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12311
#4: Protein Protein YNG1 / ING1 homolog 1


Mass: 25391.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: YNG1, YOR064C, YOR29-15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08465
#5: Protein Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 27473.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35189
#6: Protein Chromatin modification-related protein EAF6 / ESA1-associated factor 6


Mass: 12915.704 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: EAF6, YJR082C, J1854 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P47128

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Non-polymers , 2 types, 6 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HAT complex / Type: COMPLEX / Entity ID: #2, #1, #3-#4 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.17.1_3660model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176266 / Num. of class averages: 6 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00511103
ELECTRON MICROSCOPYf_angle_d0.6414973
ELECTRON MICROSCOPYf_dihedral_angle_d13.9251437
ELECTRON MICROSCOPYf_chiral_restr0.0441612
ELECTRON MICROSCOPYf_plane_restr0.0051901

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