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- PDB-9rdk: Cryo-EM structure of the human SAGA co-activator complex -

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Entry
Database: PDB / ID: 9rdk
TitleCryo-EM structure of the human SAGA co-activator complex
Components
  • (Splicing factor 3B subunit ...) x 2
  • (Transcription ...) x 5
  • Ataxin-7
  • STAGA complex 65 subunit gamma
  • TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
  • TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
  • Transcriptional adapter 1
  • Transformation/transcription domain-associated protein
KeywordsTRANSCRIPTION / Transcription co-activator / Lysine acetyltransferase / complex
Function / homology
Function and homology information


SAGA-type complex / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / somitogenesis / embryonic placenta development ...SAGA-type complex / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / somitogenesis / embryonic placenta development / nucleus organization / Swr1 complex / U12-type spliceosomal complex / SAGA complex / maintenance of protein location in nucleus / RNA splicing, via transesterification reactions / splicing factor binding / U2-type precatalytic spliceosome / RNA polymerase binding / U2-type prespliceosome assembly / U2-type spliceosomal complex / regulation of double-strand break repair / U2 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / transcription preinitiation complex / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / precatalytic spliceosome / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / histone deacetylase complex / regulation of RNA splicing / mRNA Splicing - Minor Pathway / NuA4 histone acetyltransferase complex / DNA repair-dependent chromatin remodeling / limb development / gastrulation / positive regulation of transcription initiation by RNA polymerase II / U2 snRNA binding / RNA polymerase II preinitiation complex assembly / positive regulation of double-strand break repair via homologous recombination / spliceosomal snRNP assembly / visual perception / catalytic step 2 spliceosome / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / regulation of DNA repair / TBP-class protein binding / nuclear estrogen receptor binding / negative regulation of protein catabolic process / promoter-specific chromatin binding / DNA-templated transcription initiation / mRNA splicing, via spliceosome / transcription initiation at RNA polymerase II promoter / microtubule cytoskeleton organization / mRNA transcription by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / transcription by RNA polymerase II / autophagy / transcription coregulator activity / mRNA Polyadenylation / nuclear matrix / microtubule cytoskeleton / transcription corepressor activity / positive regulation of cell growth / HATs acetylate histones / Dengue Virus-Host Interactions / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / regulation of apoptotic process / regulation of cell cycle / transcription coactivator activity / nuclear speck / protein stabilization / Ub-specific processing proteases / chromatin remodeling / protein heterodimerization activity / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / identical protein binding
Similarity search - Function
STAGA complex 65 subunit gamma / : / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. ...STAGA complex 65 subunit gamma / : / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Transcription initiation factor IID, subunit 13 / : / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, 31kD subunit / Bromodomain transcription factors and PHD domain containing proteins / Transcription initiation factor TAFII31 / Bromodomain associated / Bromodomain associated domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / : / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / Splicing factor 3B subunit 5 ...Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / Splicing factor 3B subunit 5 / Transcription initiation factor TFIID subunit 9B / Transformation/transcription domain-associated protein / TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsDamilot, M. / Ben-Shem, A. / Papai, G.
Funding support France, 2items
OrganizationGrant numberCountry
La ligue contre le cancer France
Agence Nationale de la Recherche (ANR)ANR-ATAC France
CitationJournal: Sci Adv / Year: 2026
Title: Insights into the structure and evolution of the human SAGA complex by affinity-ligand purification.
Authors: Mylène Damilot / Thomas Schoeps / Laszlo Tora / Patrick Schultz / Luc Lebeau / Gabor Papai / Adam Ben-Shem /
Abstract: Human SAGA is a 20-subunit transcriptional coactivator. Compared with yeast, metazoan SAGA uniquely incorporates a 150-kDa splicing-factor module (SPL), also present in U2 small nuclear ...Human SAGA is a 20-subunit transcriptional coactivator. Compared with yeast, metazoan SAGA uniquely incorporates a 150-kDa splicing-factor module (SPL), also present in U2 small nuclear ribonucleoprotein (U2snRNP). Metazoan gene duplication further specialized shared TFIID/SAGA subunits into SAGA-specific paralogs (TAF5L and TAF6L), but the functional consequences of this divergence are unknown. We report the structure of endogenous human SAGA purified via an affinity ligand from cells that were not disturbed by any genomic engineering tools. Our work reveals the high-resolution structure of SPL and the TAF6L HEAT repeat domain that provides the SPL with a docking surface. We elucidate how SPL and the HEAT repeats are incorporated into SAGA. We identify major structural differences between TAF6L/TAF5L and their canonical paralogs that enable SPL accommodation. SPL engages SAGA through a substantially smaller interface than in U2snRNP, despite sharing a deeply inserted helical motif. The seemingly weaker interaction of SPL with SAGA raises the possibility that SAGA relays this module to the splicing machinery.
History
DepositionJun 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Transcription initiation factor TFIID subunit 9B
N: Ataxin-7
L: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
A: Splicing factor 3B subunit 3
C: Transformation/transcription domain-associated protein
D: STAGA complex 65 subunit gamma
G: Transcription initiation factor TFIID subunit 12
H: Transcription initiation factor TFIID subunit 10
I: Transcription initiation protein SPT3 homolog
J: Transcriptional adapter 1
K: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
M: Transcription factor SPT20 homolog
B: Splicing factor 3B subunit 5


Theoretical massNumber of molelcules
Total (without water)1,086,46813
Polymers1,086,46813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Transcription ... , 5 types, 5 molecules EGHIM

#1: Protein Transcription initiation factor TFIID subunit 9B / Neuronal cell death-related protein 7 / DN-7 / Transcription initiation factor TFIID subunit 9-like ...Neuronal cell death-related protein 7 / DN-7 / Transcription initiation factor TFIID subunit 9-like / Transcription-associated factor TAFII31L


Mass: 27654.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q9HBM6
#7: Protein Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII-20/TAFII-15 / TAFII20/TAFII15


Mass: 17948.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q16514
#8: Protein Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAF(II)30 / TAFII-30 / TAFII30


Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q12962
#9: Protein Transcription initiation protein SPT3 homolog / SPT3-like protein


Mass: 35840.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75486
#12: Protein Transcription factor SPT20 homolog / p38-interacting protein / p38IP


Mass: 85884.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q8NEM7

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Protein , 6 types, 6 molecules NLCDJK

#2: Protein Ataxin-7 / Spinocerebellar ataxia type 7 protein


Mass: 95597.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: O15265
#3: Protein TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / TAF5L / PCAF-associated factor 65 beta / PAF65-beta


Mass: 66223.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: O75529
#5: Protein Transformation/transcription domain-associated protein / 350/400 kDa PCAF-associated factor / PAF350/400 / STAF40 / Tra1 homolog


Mass: 438139.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q9Y4A5
#6: Protein STAGA complex 65 subunit gamma / Adenocarcinoma antigen ART1 / SPTF-associated factor 65 gamma / STAF65gamma / Suppressor of Ty 7-like


Mass: 46243.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: O94864
#10: Protein Transcriptional adapter 1 / SPT3-associated factor 42 / STAF42 / Transcriptional adapter 1-like protein


Mass: 37432.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q96BN2
#11: Protein TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L / TAF6L / PCAF-associated factor 65-alpha / PAF65-alpha


Mass: 67903.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q9Y6J9

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Splicing factor 3B subunit ... , 2 types, 2 molecules AB

#4: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q15393
#13: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: Q9BWJ5

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Details

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: SAGA / Type: COMPLEX / Entity ID: #4, #13, #5-#6, #1, #7-#11, #3, #12, #2 / Source: NATURAL
Molecular weightValue: 1.6 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human) / Strain: K562
Buffer solutionpH: 8
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
2SerialEMimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1027610
3D reconstructionResolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272167 / Symmetry type: POINT

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