3MHS

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Literature

Structural insights into the assembly and function of the SAGA deubiquitinating module.

Samara, N.L.Datta, A.B.Berndsen, C.E.Zhang, X.Yao, T.Cohen, R.E.Wolberger, C.

(2010) Science 328: 1025-1029

  • DOI: 10.1126/science.1190049
  • Primary Citation of Related Structures:  
    3MHH, 3MHS

  • PubMed Abstract: 
  • SAGA is a transcriptional coactivator complex that is conserved across eukaryotes and performs multiple functions during transcriptional activation and elongation. One role is deubiquitination of histone H2B, and this activity resides in a distinct subcomplex called the deubiquitinating module (DUBm), which contains the ubiquitin-specific protease Ubp8, bound to Sgf11, Sus1, and Sgf73 ...

    SAGA is a transcriptional coactivator complex that is conserved across eukaryotes and performs multiple functions during transcriptional activation and elongation. One role is deubiquitination of histone H2B, and this activity resides in a distinct subcomplex called the deubiquitinating module (DUBm), which contains the ubiquitin-specific protease Ubp8, bound to Sgf11, Sus1, and Sgf73. The deubiquitinating activity depends on the presence of all four DUBm proteins. We report here the 1.90 angstrom resolution crystal structure of the DUBm bound to ubiquitin aldehyde, as well as the 2.45 angstrom resolution structure of the uncomplexed DUBm. The structure reveals an arrangement of protein domains that gives rise to a highly interconnected complex, which is stabilized by eight structural zinc atoms that are critical for enzymatic activity. The structure suggests a model for how interactions with the other DUBm proteins activate Ubp8 and allows us to speculate about how the DUBm binds to monoubiquitinated histone H2B in nucleosomes.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 8A476Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UBP8YMR223WYM9959.05
EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
UniProt
Find proteins for P50102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SUS1B96Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUS1YBR111W-A
UniProt
Find proteins for Q6WNK7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SAGA-associated factor 11C99Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SGF11YPL047W
UniProt
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinD76Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA52UBBUBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
SAGA-associated factor 73E96Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SGF73YGL066W
UniProt
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.6α = 90
b = 102.084β = 90
c = 120.903γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SHELXDphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance