9VKW: NuA3 complex

Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A. Determined by electron microscopy at 3.13 Å resolution. Released 10 Dec 2025.

Method
Electron microscopy
Resolution
3.13 Å
Organism
Saccharomyces cerevisiae S288C
Chains
5
Atoms
10,735
Mol. weight
250.72 kDa
Ligands
ZN, ACO
Released
10 Dec 2025

Explore 9VKW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VKW contains 55 α-helices and 33 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 15 β-strands

ElementResiduesLengthSheet
β-strand115-11951
α-helix122-1254
α-helix128-14114
α-helix154-16613
α-helix190-1934
α-helix195-1984
α-helix213-2142
α-helix216-2183
α-helix219-2279
α-helix229-2368
β-strand275-27622
β-strand28013
β-strand28212
α-helix283-2842
α-helix292-2954
β-strand300-30232
β-strand309-31022
α-helix313-3208
β-strand331-33664
β-strand339-34464
α-helix352-3609
β-strand376-385104
β-strand397-407114
β-strand418-42144
α-helix423-4253
α-helix430-44415
α-helix457-48529
β-strand49415
α-helix499-5068
α-helix510-52011
β-strand523-52426
β-strand540-54126
α-helix546-55712
α-helix566-5683
α-helix589-5935
α-helix679-68911
α-helix694-6952
β-strand69615
α-helix6971
Chain B: 20 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand66-6837
β-strand78-8037
β-strand9313
α-helix98-1003
α-helix115-1206
α-helix132-1398
α-helix159-1613
α-helix162-17211
α-helix176-1783
α-helix191-20111
α-helix209-22719
α-helix235-25117
β-strand280-28238
β-strand289-29138
α-helix292-2954
α-helix308-3125
β-strand330-33129
β-strand333110
β-strand339-34029
α-helix343-3464
β-strand351-352210
β-strand361-362210
α-helix371-3733
β-strand387111
β-strand398111
α-helix400-4067
β-strand409-411312
α-helix417-4226
α-helix429-4313
β-strand432-434312
α-helix447-46418
β-strand487113
β-strand493113
α-helix497-51014
α-helix516-53318
α-helix552-60150
Chain C: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix13-153
α-helix18-214
α-helix23-4119
α-helix47-9751
Chain D: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix12-4534
α-helix47-526
α-helix100-10910
Chain E: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix179-1868
α-helix191-20313
β-strand211-21441
β-strand219-22351
α-helix224-2263
α-helix229-24315

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Histone acetyltransferase SAS3Aprotein831Saccharomyces cerevisiae S288CP34218 (AlphaFold model)
NuA3 HAT complex component NTO1Bprotein748Saccharomyces cerevisiae S288CQ12311 (AlphaFold model)
Protein YNG1Cprotein219Saccharomyces cerevisiae S288CQ08465 (AlphaFold model)
Transcription initiation factor TFIID subunit 14Eprotein244Saccharomyces cerevisiae S288CP35189 (AlphaFold model)
Chromatin modification-related protein EAF6Dprotein113Saccharomyces cerevisiae S288CP47128
Sequence of entity 1 (A), FASTA
>9VKW_1 Histone acetyltransferase SAS3 (chains A)
MSLTANDESPKPKKNALLKNLEIDDLIHSQFVRSDTNGHRTTRRLFNSDASISHRIRGSV
RSDKGLNKIKKGLISQQSKLASENSSQNIVNRDNKMGAVSFPIIEPNIEVSEELKVRIKY
DSIKFFNFERLISKSSVIAPLVNKNITSSGPLIGFQRRVNRLKQTWDLATENMEYPYSSD
NTPFRDNDSWQWYVPYGGTIKKMKDFSTKRTLPTWEDKIKFLTFLENSKSATYINGNVSL
CNHNETDQENEDRKKRKGKVPRIKNKVWFSQIEYIVLRNYEIKPWYTSPFPEHINQNKMV
FICEFCLKYMTSRYTFYRHQLKCLTFKPPGNEIYRDGKLSVWEIDGRENVLYCQNLCLLA
KCFINSKTLYYDVEPFIFYILTEREDTENHPYQNAAKFHFVGYFSKEKFNSNDYNLSCIL
TLPIYQRKGYGQFLMEFSYLLSRKESKFGTPQKPLSDLGLLTYRTFWKIKCAEVLLKLRD
SARRRSNNKNEDTFQQVSLNDIAKLTGMIPTDVVFGLEQLQVLYRHKTRSLSSLDDFNYI
IKIDSWNRIENIYKTWSSKNYPRVKYDKLLWEPIILGPSFGINGMMNLEPTALADEALTN
ETMAPVISNNTHIENYNNSRAHNKRRRRRRRSSEHKTSKLHVNNIIEPEVPATDFFEDTV
SSLTEYMCDYKNTNNDRLIYQAEKRVLESIHDRKGIPRSKFSTETHWELCFTIKNSETPL
GNHAARRNDTGISSLEQDEVENDVDTELYVGENAKEDEDEDEDFTLDDDIEDEQISEEND
EEEDTYEEDSDDDEDGKRKGQEQDENDIESHIRKERVRKRRKITLIEDDEE
Sequence of entity 2 (B), FASTA
>9VKW_2 NuA3 HAT complex component NTO1 (chains B)
MNRGSLDDGPKLREEKHFQDFYPDLNADTLLPFIVPLVETKDNSTDTDSDDISNRNNREI
GSVKSVQTKELIFKGRVTTEPLVLKKNEVEFQKCKITTNELKGKKNPYCVRFNESFISRY
YHINKVRNRKSYKQQQKEFDGVEAPYFTKFSSKEAPNITISTSTKSAIQKFASISPNLVN
FKPQYDMDEQDELYLHYLNKRYFKDQMSHEIFEILMTTLETEWFHIEKHIPSTNSLIARH
NILRDCKNYELYGSDDGTGLSMDQACAVCLGTDSDNLNTIVFCDGCDIAVHQECYGIIFI
PEGKWLCRRCMISKNNFATCLMCPSHTGAFKQTDTGSWVHNICALWLPELYFSNLHYMEP
IEGVQNVSVSRWKLNCYICKKKMGACIQCFQRNCFTAYHVTCARRAGLYMSKGKCTIQEL
ASNQFSQKYSVESFCHKHAPRGWQTSIEGINKARKYFSLLSTLQTETPQHNEANDRTNSK
FNKTIWKTPNQTPVAPHVFAEILQKVVDFFGLANPPAGAFDICKYWSMKRELTGGTPLTA
CFENNSLGSLTEEQVQTRIDFANDQLEDLYRLKELTTLVKKRTQASNSLSRSRKKVFDIV
KSPQKYLLKINVLDIFIKSEQFKALERLVTEPKLLVILEKCKHCDFDTVQIFKEEIMHFF
EVLETLPGASRILQTVSSKAKEQVTNLIGLIEHVDIKKLLSRDFIINDDKIEERPWSGPV
IMEEEGLSDAEELSAGEHRMLKLILNSG
Sequence of entity 3 (C), FASTA
>9VKW_3 Protein YNG1 (chains C)
MEHLANENSDSDIRYSFLSTLDHLPCELIRSLRLMQTIDLFKNEEDEPGMERACRDLLLV
ATYINDLVDDQIHFLKQHKKELEIQKSVTKNFNSSLENIKSKLTLEEPGAYKEPKLLLKI
NLKKAKSRERKESITSPTIGINQGDVTEGNNNQEEVYCFCRNVSYGPMVACDNPACPFEW
FHYGCVGLKQAPKGKWYCSKDCKEIANQRSKSKRQKRRK
Sequence of entity 4 (E), FASTA
>9VKW_4 Transcription initiation factor TFIID subunit 14 (chains E)
MVATVKRTIRIKTQQHILPEVPPVENFPVRQWSIEIVLLDDEGKEIPATIFDKVIYHLHP
TFANPNRTFTDPPFRIEEQGWGGFPLDISVFLLEKAGERKIPHDLNFLQESYEVEHVIQI
PLNKPLLTEELAKSGSTEETTANTGTIGKRRTTTNTTAEPKAKRAKTGSASTVKGSVDLE
KLAFGLTKLNEDDLVGVVQMVTDNKTPEMNVTNNVEEGEFIIDLYSLPEGLLKSLWDYVK
KNTE
Sequence of entity 5 (D), FASTA
>9VKW_5 Chromatin modification-related protein EAF6 (chains D)
MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHG
SKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn4
ACOAcetyl coenzyme *aC23 H38 N7 O17 P3 S1

Primary citation

Mechanistic insights into histone recognition and H3K14 acetylation by the NuA3 histone acetyltransferase complex. Shi, W., Zhao, L., Wang, Y. et al. Nat Commun (2025) 17:342-342. DOI 10.1038/s41467-025-67049-0 · PubMed

Other PDB entries of the same protein (UniProt P34218 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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