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- EMDB-64517: The NuA3 histone acetyltransferase complex bound to acetyl-CoA an... -

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Basic information

Entry
Database: EMDB / ID: EMD-64517
TitleThe NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail
Map data
Sample
  • Complex: HAT complex
    • Protein or peptide: Histone acetyltransferase SAS3
    • Protein or peptide: Histone H3
    • Protein or peptide: NuA3 HAT complex component NTO1
    • Protein or peptide: Protein YNG1
  • Protein or peptide: Transcription initiation factor TFIID subunit 14
  • Protein or peptide: Chromatin modification-related protein EAF6
  • Ligand: ZINC ION
  • Ligand: ACETYL COENZYME *A
KeywordsDNA / nucleosome / histone acetylation / METAL BINDING PROTEIN
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / PI5P Regulates TP53 Acetylation / 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 / histone H3K36me3 reader activity / Platelet degranulation / SUMOylation of transcription cofactors ...NuA3b histone acetyltransferase complex / PI5P Regulates TP53 Acetylation / 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 / 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 / kinetochore assembly / 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 / rRNA transcription / subtelomeric heterochromatin formation / intracellular copper ion homeostasis / nucleolar large rRNA transcription by RNA polymerase I / mitotic metaphase chromosome alignment / histone acetyltransferase / RNA polymerase II preinitiation complex assembly / CENP-A containing nucleosome / nucleosomal DNA binding / aerobic respiration / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / kinetochore / structural constituent of chromatin / nucleosome / transcription by RNA polymerase II / chromatin organization / heterochromatin formation / histone binding / 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 / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / DNA binding / zinc ion binding / identical protein 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
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 (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang YR / Zhang HQ
Funding support1 items
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, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64517.png

Downloads & links

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Map

FileDownload / File: emd_64517.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 290 pix.
= 279.647 Å		0.96 Å/pix.
x 290 pix.
= 279.647 Å		0.96 Å/pix.
x 290 pix.
= 279.647 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9643 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.278
Minimum - Maximum-1.3735554 - 1.9599421
Average (Standard dev.)0.00042177332 (±0.03801375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 279.647 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64517_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64517_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : HAT complex

EntireName: HAT complex
Components
  • Complex: HAT complex
    • Protein or peptide: Histone acetyltransferase SAS3
    • Protein or peptide: Histone H3
    • Protein or peptide: NuA3 HAT complex component NTO1
    • Protein or peptide: Protein YNG1
  • Protein or peptide: Transcription initiation factor TFIID subunit 14
  • Protein or peptide: Chromatin modification-related protein EAF6
  • Ligand: ZINC ION
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: HAT complex

SupramoleculeName: HAT complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #3-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 2.263667 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
ARTKQTARKS TGGMAPRKQL A

UniProtKB: Histone H3

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Macromolecule #2: Histone acetyltransferase SAS3

MacromoleculeName: Histone acetyltransferase SAS3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 97.723445 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLTANDESP KPKKNALLKN LEIDDLIHSQ FVRSDTNGHR TTRRLFNSDA SISHRIRGSV RSDKGLNKIK KGLISQQSKL ASENSSQNI VNRDNKMGAV SFPIIEPNIE VSEELKVRIK YDSIKFFNFE RLISKSSVIA PLVNKNITSS GPLIGFQRRV N RLKQTWDL ...String:
MSLTANDESP KPKKNALLKN LEIDDLIHSQ FVRSDTNGHR TTRRLFNSDA SISHRIRGSV RSDKGLNKIK KGLISQQSKL ASENSSQNI VNRDNKMGAV SFPIIEPNIE VSEELKVRIK YDSIKFFNFE RLISKSSVIA PLVNKNITSS GPLIGFQRRV N RLKQTWDL ATENMEYPYS SDNTPFRDND SWQWYVPYGG TIKKMKDFST KRTLPTWEDK IKFLTFLENS KSATYINGNV SL CNHNETD QENEDRKKRK GKVPRIKNKV WFSQIEYIVL RNYEIKPWYT SPFPEHINQN KMVFICEFCL KYMTSRYTFY RHQ LKCLTF KPPGNEIYRD GKLSVWEIDG RENVLYCQNL CLLAKCFINS KTLYYDVEPF IFYILTERED TENHPYQNAA KFHF VGYFS KEKFNSNDYN LSCILTLPIY QRKGYGQFLM EFSYLLSRKE SKFGTPEKPL SDLGLLTYRT FWKIKCAEVL LKLRD SARR RSNNKNEDTF QQVSLNDIAK LTGMIPTDVV FGLEQLQVLY RHKTRSLSSL DDFNYIIKID SWNRIENIYK TWSSKN YPR VKYDKLLWEP IILGPSFGIN GMMNLEPTAL ADEALTNETM APVISNNTHI ENYNNSRAHN KRRRRRRRSS EHKTSKL HV NNIIEPEVPA TDFFEDTVSS LTEYMCDYKN TNNDRLIYQA EKRVLESIHD RKGIPRSKFS TETHWELCFT IKNSETPL G NHAARRNDTG ISSLEQDEVE NDVDTELYVG ENAKEDEDED EDFTLDDDIE DEQISEENDE EEDTYEEDSD DDEDGKRKG QEQDENDIES HIRKERVRKR RKITLIEDDE E

UniProtKB: Histone acetyltransferase SAS3

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Macromolecule #3: NuA3 HAT complex component NTO1

MacromoleculeName: NuA3 HAT complex component NTO1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 85.102188 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: KLREEKHFQD FYPDLNADTL LPFIVPLVET KDNSTDTDSD DISNRNNREI GSVKSVQTKE LIFKGRVTTE PLVLKKNEVE FQKCKITTN ELKGKKNPYC VRFNESFISR YYHINKVRNR KSYKQQQKEF DGVEAPYFTK FSSKEAPNIT ISTSTKSAIQ K FASISPNL ...String:
KLREEKHFQD FYPDLNADTL LPFIVPLVET KDNSTDTDSD DISNRNNREI GSVKSVQTKE LIFKGRVTTE PLVLKKNEVE FQKCKITTN ELKGKKNPYC VRFNESFISR YYHINKVRNR KSYKQQQKEF DGVEAPYFTK FSSKEAPNIT ISTSTKSAIQ K FASISPNL VNFKPQYDMD EQDELYLHYL NKRYFKDQMS HEIFEILMTT LETEWFHIEK HIPSTNSLIA RHNILRDCKN YE LYGSDDG TGLSMDQACA VCLGTDSDNL NTIVFCDGCD IAVHQECYGI IFIPEGKWLC RRCMISKNNF ATCLMCPSHT GAF KQTDTG SWVHNICALW LPELYFSNLH YMEPIEGVQN VSVSRWKLNC YICKKKMGAC IQCFQRNCFT AYHVTCARRA GLYM SKGKC TIQELASNQF SQKYSVESFC HKHAPRGWQT SIEGINKARK YFSLLSTLQT ETPQHNEAND RTNSKFNKTI WKTPN QTPV APHVFAEILQ KVVDFFGLAN PPAGAFDICK YWSMKRELTG GTPLTACFEN NSLGSLTEEQ VQTRIDFAND QLEDLY RLK ELTTLVKKRT QASNSLSRSR KKVFDIVKSP QKYLLKINVL DIFIKSEQFK ALERLVTEPK LLVILEKCKH CDFDTVQ IF KEEIMHFFEV LETLPGASRI LQTVSSKAKE QVTNLIGLIE HVDIKKLLSR DFIINDDKIE ERPWSGPVIM EEEGLSDA E ELSAGEHRML KLILNSG

UniProtKB: NuA3 HAT complex component NTO1

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Macromolecule #4: Protein YNG1

MacromoleculeName: Protein YNG1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 25.391049 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEHLANENSD SDIRYSFLST LDHLPCELIR SLRLMQTIDL FKNEEDEPGM ERACRDLLLV ATYINDLVDD QIHFLKQHKK ELEIQKSVT KNFNSSLENI KSKLTLEEPG AYKEPKLLLK INLKKAKSRE RKESITSPTI GINQGDVTEG NNNQEEVYCF C RNVSYGPM ...String:
MEHLANENSD SDIRYSFLST LDHLPCELIR SLRLMQTIDL FKNEEDEPGM ERACRDLLLV ATYINDLVDD QIHFLKQHKK ELEIQKSVT KNFNSSLENI KSKLTLEEPG AYKEPKLLLK INLKKAKSRE RKESITSPTI GINQGDVTEG NNNQEEVYCF C RNVSYGPM VACDNPACPF EWFHYGCVGL KQAPKGKWYC SKDCKEIANQ RSKSKRQKRR K

UniProtKB: Protein YNG1

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Macromolecule #5: Transcription initiation factor TFIID subunit 14

MacromoleculeName: Transcription initiation factor TFIID subunit 14 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 27.473154 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVATVKRTIR IKTQQHILPE VPPVENFPVR QWSIEIVLLD DEGKEIPATI FDKVIYHLHP TFANPNRTFT DPPFRIEEQG WGGFPLDIS VFLLEKAGER KIPHDLNFLQ ESYEVEHVIQ IPLNKPLLTE ELAKSGSTEE TTANTGTIGK RRTTTNTTAE P KAKRAKTG ...String:
MVATVKRTIR IKTQQHILPE VPPVENFPVR QWSIEIVLLD DEGKEIPATI FDKVIYHLHP TFANPNRTFT DPPFRIEEQG WGGFPLDIS VFLLEKAGER KIPHDLNFLQ ESYEVEHVIQ IPLNKPLLTE ELAKSGSTEE TTANTGTIGK RRTTTNTTAE P KAKRAKTG SASTVKGSVD LEKLAFGLTK LNEDDLVGVV QMVTDNKTPE MNVTNNVEEG EFIIDLYSLP EGLLKSLWDY VK KNTE

UniProtKB: Transcription initiation factor TFIID subunit 14

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Macromolecule #6: Chromatin modification-related protein EAF6

MacromoleculeName: Chromatin modification-related protein EAF6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 12.915704 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MTDELKSYEA LKAELKKSLQ DRREQEDTFD NLQQEIYDKE TEYFSHNSNN NHSGHGGAHG SKSHYSGNII KGFDTFSKSH HSHADSAFN NNDRIFSLSS ATYVKQQHGQ SQND

UniProtKB: Chromatin modification-related protein EAF6

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 8 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 6 / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 176266
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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