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- PDB-9vkw: Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A -

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Basic information

Entry
Database: PDB / ID: 9vkw
TitleCryo-EM structure of the NuA3 complex bound to Ace-coenzyme A
Components
  • Chromatin modification-related protein EAF6
  • Histone acetyltransferase SAS3
  • NuA3 HAT complex component NTO1
  • Protein YNG1
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSFERASE / NuA3 / Cryo-EM / Histone / nucleosome
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / PI5P Regulates TP53 Acetylation / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / histone H3K36me3 reader activity / Platelet degranulation / SUMOylation of transcription cofactors / transcription factor TFIIF complex / mediator complex / Ino80 complex ...NuA3b histone acetyltransferase complex / PI5P Regulates TP53 Acetylation / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / histone H3K36me3 reader activity / Platelet degranulation / SUMOylation of transcription cofactors / transcription factor TFIIF complex / mediator complex / 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 / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / histone acetyltransferase / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription by RNA polymerase II / chromatin organization / histone binding / chromosome, telomeric region / chromatin remodeling / DNA repair / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / 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 / 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 / Protein YNG1 / NuA3 HAT complex component NTO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsZhang, H.Q. / Wang, Y.R.
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
DepositionJun 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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)250,72010
Polymers249,6495
Non-polymers1,0715
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 5 molecules ABCED

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


Mass: 97722.461 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
#2: Protein NuA3 HAT complex component NTO1


Mass: 86146.328 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
#3: 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
#4: 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
#5: 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, 5 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: NuA3 / Type: COMPLEX / Entity ID: #1-#5 / 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
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: FEI FALCON IV (4k 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: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134246 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310975
ELECTRON MICROSCOPYf_angle_d0.54514807
ELECTRON MICROSCOPYf_dihedral_angle_d11.1831420
ELECTRON MICROSCOPYf_chiral_restr0.0411595
ELECTRON MICROSCOPYf_plane_restr0.0041881

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