6CW3

Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2.

Sun, J.Paduch, M.Kim, S.A.Kramer, R.M.Barrios, A.F.Lu, V.Luke, J.Usatyuk, S.Kossiakoff, A.A.Tan, S.

(2018) Proc Natl Acad Sci U S A 115: 10010-10015

  • DOI: https://doi.org/10.1073/pnas.1805343115
  • Primary Citation of Related Structures:  
    6CW2, 6CW3

  • PubMed Abstract: 

    The Gcn5 histone acetyltransferase (HAT) subunit of the SAGA transcriptional coactivator complex catalyzes acetylation of histone H3 and H2B N-terminal tails, posttranslational modifications associated with gene activation. Binding of the SAGA subunit partner Ada2 to Gcn5 activates Gcn5's intrinsically weak HAT activity on histone proteins, but the mechanism for this activation by the Ada2 SANT domain has remained elusive. We have employed Fab antibody fragments as crystallization chaperones to determine crystal structures of a yeast Ada2/Gcn5 complex. Our structural and biochemical results indicate that the Ada2 SANT domain does not activate Gcn5's activity by directly affecting histone peptide binding as previously proposed. Instead, the Ada2 SANT domain enhances Gcn5 binding of the enzymatic cosubstrate acetyl-CoA. This finding suggests a mechanism for regulating chromatin modification enzyme activity: controlling binding of the modification cosubstrate instead of the histone substrate.


  • Organizational Affiliation

    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
antibody heavy chain
A, C
234Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antibody light chain
B, D
215Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase GCN5E [auth F],
G [auth H]
254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GCN5ADA4SWI9YGR252W
EC: 2.3.1.48
UniProt
Find proteins for Q03330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03330 
Go to UniProtKB:  Q03330
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UniProt GroupQ03330
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional adapter 2F [auth E],
H [auth G]
122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ADA2YDR448WD9461.33
UniProt
Find proteins for Q02336 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02336 
Go to UniProtKB:  Q02336
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UniProt GroupQ02336
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.657α = 90
b = 104.061β = 90
c = 166.335γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM088236
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111651
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU01GM094588
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM072688
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54HG006436

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence, Structure summary
  • Version 1.4: 2020-03-04
    Changes: Derived calculations