4ZUX

SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for histone H2B deubiquitination by the SAGA DUB module.

Morgan, M.T.Haj-Yahya, M.Ringel, A.E.Bandi, P.Brik, A.Wolberger, C.

(2016) Science 351: 725-728

  • DOI: https://doi.org/10.1126/science.aac5681
  • Primary Citation of Related Structures:  
    4ZUX

  • PubMed Abstract: 

    Monoubiquitinated histone H2B plays multiple roles in transcription activation. H2B is deubiquitinated by the Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator, which contains a four-protein subcomplex known as the deubiquitinating (DUB) module. The crystal structure of the Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to a ubiquitinated nucleosome reveals that the DUB module primarily contacts H2A/H2B, with an arginine cluster on the Sgf11 zinc finger domain docking on the conserved H2A/H2B acidic patch. The Ubp8 catalytic domain mediates additional contacts with H2B, as well as with the conjugated ubiquitin. We find that the DUB module deubiquitinates H2B both in the context of the nucleosome and in H2A/H2B dimers complexed with the histone chaperone, FACT, suggesting that SAGA could target H2B at multiple stages of nucleosome disassembly and reassembly during transcription.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E, K, O
136Xenopus laevisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F, L, P
103Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G, M, Q
130Xenopus laevisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H, N, R
123Xenopus laevisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 8EA [auth e],
JA [auth j],
U,
Z
472Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: UBP8YMR223WYM9959.05
EC: 3.4.19.12
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription and mRNA export factor SUS1AA [auth a],
FA [auth f],
KA [auth k],
V
96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUS1YBR111W-A
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 11BA [auth b],
GA [auth g],
LA [auth l],
W
99Saccharomyces cerevisiae YJM789Mutation(s): 0 
Gene Names: SGF11SCY_5678
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-BCA [auth c],
HA [auth h],
MA [auth m],
X
76Homo sapiensMutation(s): 0 
Gene Names: UBB
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PHAROS:  P0CG47
GTEx:  ENSG00000170315 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 73DA [auth d],
IA [auth i],
NA [auth n],
Y
104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SGF73YGL066W
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER)
I, S
145synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)
J, T
145synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth Z]
BB [auth Z]
CB [auth b]
DB [auth d]
EB [auth e]
AB [auth Z],
BB [auth Z],
CB [auth b],
DB [auth d],
EB [auth e],
FB [auth e],
GB [auth e],
HB [auth e],
IB [auth e],
JB [auth e],
KB [auth g],
LB [auth i],
MB [auth j],
NB [auth j],
OA [auth U],
OB [auth j],
PA [auth U],
PB [auth j],
QA [auth U],
QB [auth j],
RA [auth U],
RB [auth j],
SA [auth U],
SB [auth l],
TA [auth U],
TB [auth n],
UA [auth W],
VA [auth Y],
WA [auth Z],
XA [auth Z],
YA [auth Z],
ZA [auth Z]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.804α = 90
b = 179.174β = 90
c = 353.819γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Derived calculations
  • Version 1.2: 2016-03-09
    Changes: Database references