4FK5 | pdb_00004fk5

Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.212 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4FK5

This is version 1.2 of the entry. See complete history

Literature

A Role for Intersubunit Interactions in Maintaining SAGA Deubiquitinating Module Structure and Activity.

Samara, N.L.Ringel, A.E.Wolberger, C.

(2012) Structure 20: 1414-1424

  • DOI: https://doi.org/10.1016/j.str.2012.05.015
  • Primary Citation Related Structures: 
    4FIP, 4FJC, 4FK5

  • PubMed Abstract: 

    The deubiquitinating module (DUBm) of the SAGA coactivator contains the Ubp8 isopeptidase, Sgf11, Sus1, and Sgf73, which form a highly interconnected complex. Although Ubp8 contains a canonical USP catalytic domain, it is only active when in complex with the other DUBm subunits. The Sgf11 zinc finger (Sgf11-ZnF) binds near the Ubp8 active site and is essential for full activity, suggesting that the Sgf11-ZnF helps maintain the active conformation of Ubp8. We report structural and solution studies showing that deletion of the Sgf11-ZnF destabilizes incorporation of Ubp8 within the DUBm, giving rise to domain swapping with a second complex and misaligning active site residues. Activating mutations in Ubp8 that partially restore activity in the absence of the Sgf11-ZnF promote the monomeric form of the DUBm. Our data suggest an unexpected role for Sgf11 in compensating for the absence of structural features that maintain the active conformation of Ubp8.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205-2185, USA.

Macromolecule Content 

  • Total Structure Weight: 88.05 kDa 
  • Atom Count: 6,139 
  • Modeled Residue Count: 712 
  • Deposited Residue Count: 767 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 8476Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: UBP8YM9959.05YMR223W
EC: 3.4.19.12
UniProt
Find proteins for P50102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50102 
Go to UniProtKB:  P50102
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50102
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein SUS196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUS1YBR111W-A
UniProt
Find proteins for Q6WNK7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q6WNK7 
Go to UniProtKB:  Q6WNK7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WNK7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SAGA-associated factor 1199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SGF11YPL047W
UniProt
Find proteins for Q03067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03067 
Go to UniProtKB:  Q03067
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03067
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SAGA-associated factor 73D [auth E]96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SGF73YGL066W
UniProt
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53165 
Go to UniProtKB:  P53165
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53165
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth A],
N [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth C],
O [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.212 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.528α = 90
b = 104.775β = 90
c = 107.018γ = 90
Software Package:
Software NamePurpose
Locallydata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations