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- EMDB-73235: Histone Acetyl Transferase (HAT) module of ctSAGA -

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Basic information

Entry
Database: EMDB / ID: EMD-73235
TitleHistone Acetyl Transferase (HAT) module of ctSAGA
Map data
Sample
  • Complex: Minimal HAT module of ctSAGA complex
    • Protein or peptide: Putative transcriptional coactivator HFI1 protein
    • Protein or peptide: histone acetyltransferase
    • Protein or peptide: Transcriptional adapter 2
    • Protein or peptide: Uncharacterized protein
KeywordsctSAGA complex / Histone Acetyl Transferase (HAT) Module / Tra1 module and Core module / TRANSCRIPTION
Function / homology
Function and homology information


SAGA-type complex / histone H3 acetyltransferase activity / SAGA complex / histone acetyltransferase complex / histone acetyltransferase / transcription coactivator activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...SAGA-type complex / histone H3 acetyltransferase activity / SAGA complex / histone acetyltransferase complex / histone acetyltransferase / transcription coactivator activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / ADA2 ZZ-type zing finger / Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Histone acetyltransferase GCN5 ...Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / ADA2 ZZ-type zing finger / Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Histone acetyltransferase GCN5 / Myb-like domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Myb-type HTH DNA-binding domain profile. / SANT domain profile. / SANT domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Myb domain / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / GNAT domain / SANT/Myb domain / Acyl-CoA N-acyltransferase / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional adapter 2 / histone acetyltransferase / Uncharacterized protein / Putative transcriptional coactivator HFI1 protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMattoo RUH / Chen DH / Bushnell DA / Tamir S / Kornberg RD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049985 United States
CitationJournal: Mol Cell / Year: 2025
Title: Structure of the transcriptional co-activator SAGA complex, including the histone acetyltransferase module.
Authors: Rayees U H Mattoo / Dong-Hua Chen / David A Bushnell / Sagi Tamir / Roger D Kornberg /
Abstract: The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, a 1.8 MDa multi-subunit assembly comprising 19 subunits, is required for RNA polymerase II transcription in eukaryotes. The complex consists of four ...The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, a 1.8 MDa multi-subunit assembly comprising 19 subunits, is required for RNA polymerase II transcription in eukaryotes. The complex consists of four modules: transcription-associated protein 1 (Tra1), core, deubiquitination (DUB), and histone acetyltransferase (HAT). Although the structures of the Tra1, core, and DUB modules have been determined, the overall architecture of the HAT module remained elusive due to its inherent flexibility. To address this, we conducted cryo-electron microscopy (cryo-EM) analyses on SAGA purified from the thermophilic fungus Chaetomium thermophilum, yielding structures of Tra1 and core modules at 2.6 Å and three of the four HAT subunits at 3.7 Å. The structure of the HAT module was informative about the aspects of histone acetylation and the interface of HAT-core modules, contradicting earlier AlphaFold predictions. Our structure-guided genetic and biochemical analyses confirmed the roles of Ada1 and Spt7 in anchoring the HAT module within the SAGA complex.
History
DepositionOct 12, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73235.png

Downloads & links

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Map

FileDownload / File: emd_73235.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.496 Å		1.04 Å/pix.
x 256 pix.
= 266.496 Å		1.04 Å/pix.
x 256 pix.
= 266.496 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.041 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.13039805 - 0.20755506
Average (Standard dev.)0.00014745508 (±0.0044324743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73235_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_73235_half_map_2.map
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Sample components

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Entire : Minimal HAT module of ctSAGA complex

EntireName: Minimal HAT module of ctSAGA complex
Components
  • Complex: Minimal HAT module of ctSAGA complex
    • Protein or peptide: Putative transcriptional coactivator HFI1 protein
    • Protein or peptide: histone acetyltransferase
    • Protein or peptide: Transcriptional adapter 2
    • Protein or peptide: Uncharacterized protein

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Supramolecule #1: Minimal HAT module of ctSAGA complex

SupramoleculeName: Minimal HAT module of ctSAGA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: Putative transcriptional coactivator HFI1 protein

MacromoleculeName: Putative transcriptional coactivator HFI1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 52.133355 KDa
SequenceString: MVDINPAALS RPSIGLSTPS FPGKSGSINV SVPSSASASA SASSAHSKPQ KTSLVPPRID LEPIYTALKA AIGAEQWPVY KETLTNFLI GRLNQAELSE RIDPILASQD GQKEHLHNQL IAAIYANVTR EMPDPGLAPW VSANDKPTTA QTKPVTGDAN E RRLKGEVM ...String:
MVDINPAALS RPSIGLSTPS FPGKSGSINV SVPSSASASA SASSAHSKPQ KTSLVPPRID LEPIYTALKA AIGAEQWPVY KETLTNFLI GRLNQAELSE RIDPILASQD GQKEHLHNQL IAAIYANVTR EMPDPGLAPW VSANDKPTTA QTKPVTGDAN E RRLKGEVM QLPARDRRRI KELAHNDFDP YDALANVLME HARAKPPKIA EPPASAGGLK MNFDLEIRKR YAQPLAVESG EF PDTSNIE SRMLPFCYEA GLSSGHAPDA AQFMSIATET FIKEVMSAIF SRTRSNGPGD SGSAGFGLGS GWIQTHRYRK QLA KEEEAF QRGEISRDKM GLLPVEAKAA SERGPLGMAD VRLALEMGDC GLAGFPVIVK SVIYGWREGE LENWEDYTYV DPSR PDGIA IPSRGDGDVE MGGVGVNGVV KGEPEPQQQP LANGVHDVDA MDIDGVSVAG GAANEIWWEG AEPETSDLLN AVLDS CLAV N

UniProtKB: Putative transcriptional coactivator HFI1 protein

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Macromolecule #2: histone acetyltransferase

MacromoleculeName: histone acetyltransferase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 46.983691 KDa
SequenceString: MTSENGKRKA TEEPGSPSAA KRIKQEPSET DKDKKEENKD KKTVAKPPPI PYPEKPAVIE ERNGEIEFRV VNNDGERESL IILTGLKCI FQKQLPKMPK DYIARLVYDR THLSIAIVKK PLEVVGGITY RPFKNRKFAE IVFCAISSDQ QVKGYGAHLM S HLKDYVKA ...String:
MTSENGKRKA TEEPGSPSAA KRIKQEPSET DKDKKEENKD KKTVAKPPPI PYPEKPAVIE ERNGEIEFRV VNNDGERESL IILTGLKCI FQKQLPKMPK DYIARLVYDR THLSIAIVKK PLEVVGGITY RPFKNRKFAE IVFCAISSDQ QVKGYGAHLM S HLKDYVKA TTNIEHFLTY ADNYAIGYFK KQGFTKEITL DKSVWMGYIK DYEGGTIMQC TMIPRIRYLE QGRMLLKQKE CV QAKIRAF SKSHIVHPPP KQWRNGNVTP IDPLSIDAIR ESGWSPDMDE LARQPRHGPN YNQLLHLLND MQNHASSWPF LVP VNKDEV VDYYDIIKEP MDLSTMESKL EADQYQTPED FIRDAKLIFD NCRKYNNENT PYAKSANKLE KFMWQQIRQI PEWS HLEPS

UniProtKB: histone acetyltransferase

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Macromolecule #3: Transcriptional adapter 2

MacromoleculeName: Transcriptional adapter 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 58.86607 KDa
SequenceString: MGVIRKKIAG RSGEGGVKYI CDVCSVDITS TVRIRCADPA CHDYDLCVPC FANGSSSNAH KPATHSFRVI EQNSFPIFDP DWGADEELL LLEGAEIYGL GSWADIADHI GGYRTKDEVR DHYLKVYIES PNFPLPERCS PYDLELPNSI SREEFQARKK R RIEERREA ...String:
MGVIRKKIAG RSGEGGVKYI CDVCSVDITS TVRIRCADPA CHDYDLCVPC FANGSSSNAH KPATHSFRVI EQNSFPIFDP DWGADEELL LLEGAEIYGL GSWADIADHI GGYRTKDEVR DHYLKVYIES PNFPLPERCS PYDLELPNSI SREEFQARKK R RIEERREA AKNAPPPQPK TKPTASIPAC HEIQGYMPGR LEFETEYCNE AEEAVQLMSF DPGDGINPRT GELEPEMELK LT VMEIYNN RLTQRVERKK VIFEHNLLEY RENTKAEKKR SREERELLNK AKPFARMMNR HDFEQFCQGL IDELNLRQAI AQL QEWRSM RIGDLKSGEK YEQEKALRIQ KSMPMGSLDR ERLATSQRGK NQQQPEPPSG AALLVAPELP ARYKEPIIDA NGFP RPDAN RLTVDGGSVV VANGTSQPKP KYVPPPVPGV QPMNLTQDNA PDLHLLTPEE IKLCETLRIQ PKPYIMIKEQ ILKEA VKGN GSLKKKQAKE ICRLDSQKGG RIFDFMVNAG WVVKA

UniProtKB: Transcriptional adapter 2

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Macromolecule #4: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 79.972164 KDa
SequenceString: MAPSSSQKGT GKKAGSAASA IRSHQQHSQQ QRSRNTTPGP AGIPPTSSTS VSVSVASLPP IETVETETLD LRFDTFRNVT FEDLVDPAA ASALIPDSKS LDGIISRLQR LADIIEKRGA NCDRGMRLLA QTRRQRLDEL AVERGREEER RQAEADDEKK A NKKKRKAD ...String:
MAPSSSQKGT GKKAGSAASA IRSHQQHSQQ QRSRNTTPGP AGIPPTSSTS VSVSVASLPP IETVETETLD LRFDTFRNVT FEDLVDPAA ASALIPDSKS LDGIISRLQR LADIIEKRGA NCDRGMRLLA QTRRQRLDEL AVERGREEER RQAEADDEKK A NKKKRKAD SLAPGAVNTE RSSPNRESTS KARKLDRDDT ASSSLSPAAA GTPSNMDVDD KDKEKDKDKT KAEADSDSDS DD GAPPPPP RPPANVFGDD PSTFPDPTVY EIRPVLPGMS EEEIKEIYSV ASYPKSDLAH LTCGEPPDRD FSNSKPTNQI NFS TFSSYI EPYFRPFTEE DLAFLRERGD RVTPFIMPKR GKKHYTEIWA EEDGAMAIDS SPPGGRDRLP PNQARGSIDN MDDE VAETD KLSVGPLLTR LLQAMRPENR APTADDKSGP NGTSGDGDGP QQSFDFNDST AAPNPSQSQP NGVNGVAATT NGDSQ QQQQ QQQHQSLPPA TFMPESNTEA WKKATHPKLD YNQVDERIKQ ELRHIGFLPL PPSSATDPSN SSASVTPAAP PPPGTT ATT AEYDGHYDDE VAARLRVLQA RLREQILLNG ARKARLTELV KERMAYQEYQ TILEDLDAQV NAAYLKRTRT MGKKPKK NR PGQHSSGSAA AAAAAAAGMA RPGIGDLART LMDRRRRWIE QIGAVFDDEG ITKCPRVEDG DTSIFGREIM AELIKREK E AWDEEVEEE

UniProtKB: Uncharacterized protein

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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: 7.5
Sugar embeddingMaterial: HEPES Buffer
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.9 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: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 627924
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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