Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 18-mer - A2B2C2D2E2F2G2H2I2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 18-mer -A6B2C2D2E2F2G2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 18-mer - A2B2C2D2E2F2G2H2I2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 18-mer -A6B2C2D2E2F2G2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 784450.19 
• Atom Count: 49079 
• Residue Count: 5936 
• Unique protein chains: 9
• Unique nucleic acid chains: 2

4ZUX

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

• DOI: 10.2210/pdb4ZUX/pdb
• NDB: 4ZUX

• Classification: Hydrolase/DNA
• Organism(s): synthetic construct, Saccharomyces cerevisiae (strain YJM789), Xenopus laevis, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2015-05-17 Released: 2016-02-24 
• Deposition Author(s): Morgan, M., Wolberger, C.

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Experimental Data Snapshot

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

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

• PubMed: 26912860 
• DOI: 10.1126/science.aac5681


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.2	A, E, K, O	136	Xenopus laevis	Mutation(s): 0
Find proteins for P84233 (Xenopus laevis) Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F, L, P	103	Xenopus laevis	Mutation(s): 0
Find proteins for P62799 (Xenopus laevis) Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1	C, G, M, Q	130	Xenopus laevis	Mutation(s): 0
Find proteins for P06897 (Xenopus laevis) Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B 1.1	D, H, N, R	123	Xenopus laevis	Mutation(s): 0
Find proteins for P02281 (Xenopus laevis) Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin carboxyl-terminal hydrolase 8	U, Z, e, j	472	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 1  Gene Names: UBP8 EC: 3.4.19.12
Find proteins for P50102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P50102

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Transcription and mRNA export factor SUS1	V, a, f, k	96	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: SUS1
Find proteins for Q6WNK7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q6WNK7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
SAGA-associated factor 11	W, b, g, l	99	Saccharomyces cerevisiae (strain YJM789)	Mutation(s): 0  Gene Names: SGF11
Find proteins for A6ZWK1 (Saccharomyces cerevisiae (strain YJM789)) Go to UniProtKB:  A6ZWK1

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	X, c, h, m	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
SAGA-associated factor 73	Y, d, i, n	104	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: SGF73
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P53165

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (145-MER)	I,S	145	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism
DNA (145-MER)	J,T	145	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	b, d, e, g, i, j, l, n, U, W, Y, 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 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 178.804	α = 90.00
b = 179.174	β = 90.00
c = 353.819	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-17 
• Released Date: 2016-02-24 
• Deposition Author(s): Morgan, M., Wolberger, C.

Revision History 

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