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- PDB-9uuo: The NuA3 histone acetyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 9uuo
TitleThe NuA3 histone acetyltransferase complex
Components
  • Chromatin modification-related protein EAF6
  • 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 / Platelet degranulation / SUMOylation of transcription cofactors / transcription factor TFIIF complex / mediator complex / Ino80 complex / histone H3K4me3 reader activity ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / 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 / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / : / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / chromatin organization / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / chromatin remodeling / 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 / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
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: 3.68 Å
AuthorsShi, W.P. / Wang, Y.R. / Zhang, H.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Apo HAT complex
Authors: Shi, W.P. / Wang, Y.R. / Zhang, H.Q.
History
DepositionMay 7, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)250,04211
Polymers249,6505
Non-polymers3926
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 , 5 types, 5 molecules ABCFE

#1: 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
#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 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
#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

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Non-polymers , 1 types, 6 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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: #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

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: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89035 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00511251
ELECTRON MICROSCOPYf_angle_d0.59415183
ELECTRON MICROSCOPYf_dihedral_angle_d10.931455
ELECTRON MICROSCOPYf_chiral_restr0.0421634
ELECTRON MICROSCOPYf_plane_restr0.0041941

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