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- EMDB-65145: Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A -

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Basic information

Entry
Database: EMDB / ID: EMD-65145
TitleCryo-EM structure of the NuA3 complex bound to Ace-coenzyme A
Map data
Sample
  • Complex: NuA3
    • Protein or peptide: Histone acetyltransferase SAS3
    • 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
KeywordsNuA3 / Cryo-EM / Histone / nucleosome / TRANSFERASE
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / SUMOylation of transcription cofactors / Platelet degranulation / 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 / SUMOylation of transcription cofactors / Platelet degranulation / 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 / histone acetyltransferase / RNA polymerase II preinitiation complex assembly / 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 / 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
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 (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsZhang HQ / Wang YR
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the NuA3 complex bound to Acetyl-coenzyme A
Authors: Wang YR / Zhang HQ
History
DepositionJun 24, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65145.png

Downloads & links

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Map

FileDownload / File: emd_65145.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 280 pix.
= 270.004 Å		0.96 Å/pix.
x 280 pix.
= 270.004 Å		0.96 Å/pix.
x 280 pix.
= 270.004 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9643 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.7847701 - 2.3398054
Average (Standard dev.)0.000036425135 (±0.046760842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 270.004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65145_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_65145_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NuA3

EntireName: NuA3
Components
  • Complex: NuA3
    • Protein or peptide: Histone acetyltransferase SAS3
    • 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: NuA3

SupramoleculeName: NuA3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Histone acetyltransferase SAS3

MacromoleculeName: Histone acetyltransferase SAS3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 97.722461 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 SKFGTPQKPL 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 #2: NuA3 HAT complex component NTO1

MacromoleculeName: NuA3 HAT complex component NTO1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 86.146328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNRGSLDDGP KLREEKHFQD FYPDLNADTL LPFIVPLVET KDNSTDTDSD DISNRNNREI GSVKSVQTKE LIFKGRVTTE PLVLKKNEV EFQKCKITTN ELKGKKNPYC VRFNESFISR YYHINKVRNR KSYKQQQKEF DGVEAPYFTK FSSKEAPNIT I STSTKSAI ...String:
MNRGSLDDGP KLREEKHFQD FYPDLNADTL LPFIVPLVET KDNSTDTDSD DISNRNNREI GSVKSVQTKE LIFKGRVTTE PLVLKKNEV EFQKCKITTN ELKGKKNPYC VRFNESFISR YYHINKVRNR KSYKQQQKEF DGVEAPYFTK FSSKEAPNIT I STSTKSAI QKFASISPNL VNFKPQYDMD EQDELYLHYL NKRYFKDQMS HEIFEILMTT LETEWFHIEK HIPSTNSLIA RH NILRDCK NYELYGSDDG TGLSMDQACA VCLGTDSDNL NTIVFCDGCD IAVHQECYGI IFIPEGKWLC RRCMISKNNF ATC LMCPSH TGAFKQTDTG SWVHNICALW LPELYFSNLH YMEPIEGVQN VSVSRWKLNC YICKKKMGAC IQCFQRNCFT AYHV TCARR AGLYMSKGKC TIQELASNQF SQKYSVESFC HKHAPRGWQT SIEGINKARK YFSLLSTLQT ETPQHNEAND RTNSK FNKT IWKTPNQTPV APHVFAEILQ KVVDFFGLAN PPAGAFDICK YWSMKRELTG GTPLTACFEN NSLGSLTEEQ VQTRID FAN DQLEDLYRLK ELTTLVKKRT QASNSLSRSR KKVFDIVKSP QKYLLKINVL DIFIKSEQFK ALERLVTEPK LLVILEK CK HCDFDTVQIF KEEIMHFFEV LETLPGASRI LQTVSSKAKE QVTNLIGLIE HVDIKKLLSR DFIINDDKIE ERPWSGPV I MEEEGLSDAE ELSAGEHRML KLILNSG

UniProtKB: NuA3 HAT complex component NTO1

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Macromolecule #3: Protein YNG1

MacromoleculeName: Protein YNG1 / type: protein_or_peptide / ID: 3 / 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 #4: Transcription initiation factor TFIID subunit 14

MacromoleculeName: Transcription initiation factor TFIID subunit 14 / type: protein_or_peptide / ID: 4 / 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 #5: Chromatin modification-related protein EAF6

MacromoleculeName: Chromatin modification-related protein EAF6 / type: protein_or_peptide / ID: 5 / 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 #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 7 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 134246
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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