9RDK | pdb_00009rdk

Cryo-EM structure of the human SAGA co-activator complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Insights into the structure and evolution of the human SAGA complex by affinity-ligand purification.

Damilot, M.Schoeps, T.Tora, L.Schultz, P.Lebeau, L.Papai, G.Ben-Shem, A.

(2026) Sci Adv 12: eaec8104-eaec8104

  • DOI: https://doi.org/10.1126/sciadv.aec8104
  • Primary Citation Related Structures: 
    9RDK

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9BA [auth E]251Homo sapiensMutation(s): 0 
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PHAROS:  Q9HBM6
GTEx:  ENSG00000187325 
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UniProt GroupQ9HBM6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ataxin-7B [auth N]892Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163635 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5LC [auth L]589Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135801 
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UniProt GroupO75529
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3D [auth A]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transformation/transcription domain-associated proteinE [auth C]3,859Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000196367 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
STAGA complex 65 subunit gammaF [auth D]414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000119760 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120656 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166337 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation protein SPT3 homolog317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000196284 
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UniProt GroupO75486
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional adapter 1335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000152382 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L622Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162227 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor SPT20 homologL [auth M]779Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102710 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5M [auth B]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
La ligue contre le cancerFrance--
Agence Nationale de la Recherche (ANR)FranceANR-ATAC

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-01
    Type: Initial release