7KTR

Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the human SAGA coactivator complex.

Herbst, D.A.Esbin, M.N.Louder, R.K.Dugast-Darzacq, C.Dailey, G.M.Fang, Q.Darzacq, X.Tjian, R.Nogales, E.

(2021) Nat Struct Mol Biol 28: 989-996

  • DOI: https://doi.org/10.1038/s41594-021-00682-7
  • Primary Citation of Related Structures:  
    7KTR, 7KTS

  • PubMed Abstract: 

    The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP 6 ) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.


  • Organizational Affiliation

    California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein3,195Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4A5 (Homo sapiens)
Explore Q9Y4A5 
Go to UniProtKB:  Q9Y4A5
PHAROS:  Q9Y4A5
GTEx:  ENSG00000196367 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4A5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L589Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75529 (Homo sapiens)
Explore O75529 
Go to UniProtKB:  O75529
PHAROS:  O75529
GTEx:  ENSG00000135801 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75529
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of Transcription factor SPT20 homolog811Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEM7 (Homo sapiens)
Explore Q8NEM7 
Go to UniProtKB:  Q8NEM7
PHAROS:  Q8NEM7
GTEx:  ENSG00000102710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEM7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma,DhaA704Homo sapiensunclassified Rhodococcus (in: high G+C Gram-positive bacteria)Mutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O94864 (Homo sapiens)
Explore O94864 
Go to UniProtKB:  O94864
PHAROS:  O94864
GTEx:  ENSG00000119760 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94864
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9B251Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBM6 (Homo sapiens)
Explore Q9HBM6 
Go to UniProtKB:  Q9HBM6
PHAROS:  Q9HBM6
GTEx:  ENSG00000187325 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HBM6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L622Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6J9 (Homo sapiens)
Explore Q9Y6J9 
Go to UniProtKB:  Q9Y6J9
PHAROS:  Q9Y6J9
GTEx:  ENSG00000162227 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6J9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12161Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16514 (Homo sapiens)
Explore Q16514 
Go to UniProtKB:  Q16514
PHAROS:  Q16514
GTEx:  ENSG00000120656 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16514
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10218Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q12962 (Homo sapiens)
Explore Q12962 
Go to UniProtKB:  Q12962
PHAROS:  Q12962
GTEx:  ENSG00000166337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12962
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog299Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75486 (Homo sapiens)
Explore O75486 
Go to UniProtKB:  O75486
PHAROS:  O75486
GTEx:  ENSG00000196284 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75486
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional adapter 1335Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BN2 (Homo sapiens)
Explore Q96BN2 
Go to UniProtKB:  Q96BN2
PHAROS:  Q96BN2
GTEx:  ENSG00000152382 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BN2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ataxin-7K [auth N]892Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15265 (Homo sapiens)
Explore O15265 
Go to UniProtKB:  O15265
PHAROS:  O15265
GTEx:  ENSG00000163635 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15265
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
L [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18.2-3874

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesCC30250
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127018
European Molecular Biology Organization (EMBO)European UnionALTF 1002-2018
Swiss National Science FoundationSwitzerlandP2BSP3_181878
Howard Hughes Medical Institute (HHMI)United StatesCC34430
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM098218

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2021-12-08
    Changes: Database references
  • Version 1.3: 2021-12-22
    Changes: Database references