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: 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 ...

    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. cwolberg@jhmi.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E, K, O136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F, L, P103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G, M, Q130Xenopus laevisMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H, N, R123Xenopus laevisMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 8U, Z, EA [auth e], JA [auth j]472Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: UBP8YMR223WYM9959.05
EC: 3.4.19.12
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription and mRNA export factor SUS1V, AA [auth a], FA [auth f], KA [auth k]96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUS1YBR111W-A
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
SAGA-associated factor 11W, BA [auth b], GA [auth g], LA [auth l]99Saccharomyces cerevisiae YJM789Mutation(s): 0 
Gene Names: SGF11SCY_5678
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BX, CA [auth c], HA [auth h], MA [auth m]76Homo sapiensMutation(s): 0 
Gene Names: UBB
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PHAROS:  P0CG47
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
SAGA-associated factor 73Y, DA [auth d], IA [auth i], NA [auth n]104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SGF73YGL066W
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I, S145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J, T145synthetic construct
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Small Molecules
Ligands 1 Unique
IDChainsName / 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] , FB [auth e] , GB [auth e] , HB [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
 Ligand Interaction
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