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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 / 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 / Condensation of Prophase Chromosomes / : / Platelet degranulation / SUMOylation of transcription cofactors / : / Assembly of the ORC complex at the origin of replication / transcription factor TFIIF complex / mediator complex / Ino80 complex / Oxidative Stress Induced Senescence / histone H3K4me3 reader activity / silent mating-type cassette heterochromatin formation / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA Polymerase I Promoter Escape / : / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / subtelomeric heterochromatin formation / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / CENP-A containing nucleosome / aerobic respiration / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / MYST, zinc finger domain / YEATS family ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / ING family / YEATS / : / : / YEATS superfamily / MYST, zinc finger domain / YEATS family / MYST family zinc finger domain / YEATS domain profile. / 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: To Be Published
Title: Apo HAT complex
Authors: Wang, Y.R. / Zhang, H.Q.
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
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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