4WA6

Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb4WA6/pdb

• Classification: hydrolase/transcription
• Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae YJM789
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-08-28 Released: 2015-03-04 
• Deposition Author(s): Wolberger, C., Yan, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution

Wolberger, C., Yan, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C2D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 175.48 kDa 
• Atom Count: 11,129 
• Modelled Residue Count: 1,364 
• Deposited Residue Count: 1,534 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 8	A, E [auth D]	476	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: UBP8, YMR223W, YM9959.05 EC: 3.4.19.12
UniProt
Find proteins for P50102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P50102  Go to UniProtKB:  P50102

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription and mRNA export factor SUS1	B, F	96	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SUS1, YBR111W-A
UniProt
Find proteins for Q6WNK7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q6WNK7  Go to UniProtKB:  Q6WNK7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SAGA-associated factor 11	C, G	99	Saccharomyces cerevisiae YJM789	Mutation(s): 0  Gene Names: SGF11, SCY_5678
UniProt
Find proteins for A6ZWK1 (Saccharomyces cerevisiae (strain YJM789)) Explore A6ZWK1  Go to UniProtKB:  A6ZWK1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SAGA-associated factor 73	D [auth E], H	96	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: SGF73, YGL066W
UniProt
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53165  Go to UniProtKB:  P53165

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth C], P [auth E], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D], V [auth G], W [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.076	α = 90
b = 68.004	β = 106.75
c = 137.858	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
Coot	model building
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Wolberger, C., Yan, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-095822

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 2.1: 2017-11-22
  Changes: Refinement description
• Version 2.2: 2019-12-25
  Changes: Author supporting evidence
• Version 2.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description