SAXSdb — 3m99

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 8

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–471	Not recorded	SAGA-associated factor 11 × 1 （Q03067） Protein SUS1 × 1 （Q6WNK7） SAGA-associated factor 73 × 1 （P53165） ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.300

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3M99	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3MHH Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module Deposited 2010-04-08	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–471（471 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1 M Na Citrate (5.2), 16% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.273
3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–471（471 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.89 Å R-free 0.208
4FIP Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–471（471 aa） Chain E 1–471（471 aa）	Mutation：S144N Mutation：S144N	ZN ZINC ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.69 Å R-free 0.264
4FJC Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–471（471 aa） Chain E 1–471（471 aa）	Not recorded	ZN ZINC ION × 14 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.83 Å R-free 0.276
4FK5 Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module Deposited 2012-06-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–471（471 aa）	Mutation：S144N	ZN ZINC ION × 8 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；sodium citrate pH 5.2, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.03 Å R-free 0.212
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–471（471 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–471（471 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–471（471 aa） Chain D 1–471（471 aa）	Not recorded	ZN ZINC ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain U 1–471（471 aa） Chain Z 1–471（471 aa）	Not recorded	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol	Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain e 1–471（471 aa） Chain j 1–471（471 aa）	Not recorded	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol	Resolution 3.82 Å R-free 0.256
6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–471（471 aa）	Mutation：C146A	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate	Resolution 2.10 Å R-free 0.249
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain K 1–471（471 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.60 Å

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBP8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 1–471

SAGA-associated factor 11

Saccharomyces cerevisiae

UniProt Q03067

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–99	Not recorded	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P50102） Protein SUS1 × 1 （Q6WNK7） SAGA-associated factor 73 × 1 （P53165） ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.300

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3M99	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LO2 Solution structure of Sgf11(63-99) zinc finger domain Deposited 2012-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 63–99（37 aa） Fragment：SGF11-type zinc finger residues 63-99	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.115；Pressure ambient NMR sample composition 0.7 mM [U-99% 13C; U-98% 15N] sgf11, 20 mM sodium phosphate, 75 mM sodium chloride, 1 mM DTT, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3MHH Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module Deposited 2010-04-08	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1 M Na Citrate (5.2), 16% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.273
3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–99（99 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.89 Å R-free 0.208
4FIP Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–72（72 aa） Fragment：UNP Residues 1-72 Chain G 1–72（72 aa） Fragment：UNP Residues 1-72	Not recorded	ZN ZINC ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.69 Å R-free 0.264
4FJC Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–99（99 aa） Fragment：UNP Residues Sgf11 1-72 Chain G 1–99（99 aa） Fragment：UNP Residues Sgf11 1-72	Not recorded	ZN ZINC ION × 14 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.83 Å R-free 0.276
4FK5 Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module Deposited 2012-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–99（99 aa）	Not recorded	ZN ZINC ION × 8 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；sodium citrate pH 5.2, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.03 Å R-free 0.212
6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–99（99 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate	Resolution 2.10 Å R-free 0.249
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain M 1–99（99 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.60 Å

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SGF11_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 1–99

Protein SUS1

Saccharomyces cerevisiae

UniProt Q6WNK7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–96	Not recorded	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P50102） SAGA-associated factor 11 × 1 （Q03067） SAGA-associated factor 73 × 1 （P53165） ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.300

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3M99	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FWB Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1M MES pH6.5, 16% PEG4K, 20% glycerol - see publication for complete details, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.235
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–96（96 aa） Chain D 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–96（96 aa） Chain H 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 1–96（96 aa） Chain L 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain O 1–96（96 aa） Chain P 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3MHH Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module Deposited 2010-04-08	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–96（96 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1 M Na Citrate (5.2), 16% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.273
3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–96（96 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.89 Å R-free 0.208
4C31 Nup1:Sac3:Sus1 complex Deposited 2013-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–96（96 aa） Chain E 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；DESCRIBED IN DETAIL IN PUBLICATION, pH 6.0	Resolution 3.00 Å R-free 0.243
4FIP Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–96（96 aa） Chain F 1–96（96 aa）	Not recorded	ZN ZINC ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.69 Å R-free 0.264
4FJC Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–96（96 aa） Chain F 1–96（96 aa）	Not recorded	ZN ZINC ION × 14 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.83 Å R-free 0.276
4FK5 Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module Deposited 2012-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–96（96 aa）	Not recorded	ZN ZINC ION × 8 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；sodium citrate pH 5.2, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.03 Å R-free 0.212
4MBE Sac3:Sus1:Cdc31:Nup1 complex Deposited 2013-08-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–96（96 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.61 Å R-free 0.236
4MBE Sac3:Sus1:Cdc31:Nup1 complex Deposited 2013-08-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–96（96 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.61 Å R-free 0.236
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–96（96 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–96（96 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–96（96 aa） Chain F 1–96（96 aa）	Not recorded	ZN ZINC ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain V 1–96（96 aa） Chain a 1–96（96 aa）	Not recorded	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol	Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain f 1–96（96 aa） Chain k 1–96（96 aa）	Not recorded	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol	Resolution 3.82 Å R-free 0.256
6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–96（96 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate	Resolution 2.10 Å R-free 0.249
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain L 1–96（96 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.60 Å

15 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUS1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–96； UniProt 1–96

SAGA-associated factor 73

Saccharomyces cerevisiae

UniProt P53165

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–104	Fragment：UNP RESIDUES: 1-104	Ubiquitin carboxyl-terminal hydrolase 8 × 1 （P50102） SAGA-associated factor 11 × 1 （Q03067） Protein SUS1 × 1 （Q6WNK7） ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.300

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3M99	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LO3 Solution structure of Sgf73(59-102) zinc finger domain Deposited 2012-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–102（44 aa） Fragment：UNP residues 59-102	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.175；Pressure ambient NMR sample composition 0.2 mM [U-98% 15N] sgf73, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 mM TCEP, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-98% 15N] sgf73, 20 mM sodium phosphate, 75 mM sodium chloride, 1 mM DTT, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2 mM [U-98% 15N] sgf73, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 mM TCEP, 100 % D2O, 100% D2O \| 100% D2O	Resolution not provided
3MHH Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module Deposited 2010-04-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–96（96 aa） Fragment：residues 1-96	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1 M Na Citrate (5.2), 16% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.273
3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–96（96 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.89 Å R-free 0.208
4FIP Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–96（96 aa） Fragment：UNP Residues 1-96 Chain H 1–96（96 aa） Fragment：UNP Residues 1-96	Not recorded	ZN ZINC ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.69 Å R-free 0.264
4FJC Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–96（96 aa） Fragment：UNP Residues 1-96 Chain H 1–96（96 aa） Fragment：UNP Residues 1-96	Not recorded	ZN ZINC ION × 14 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.83 Å R-free 0.276
4FK5 Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module Deposited 2012-06-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–96（96 aa） Fragment：UNP Residues 1-96	Not recorded	ZN ZINC ION × 8 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；sodium citrate pH 5.2, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.03 Å R-free 0.212
4W4U Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution Deposited 2014-08-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–96（96 aa）	Mutation：Y57A	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris,18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.80 Å R-free 0.241
4W4U Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution Deposited 2014-08-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–96（96 aa）	Mutation：Y57A	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris,18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.80 Å R-free 0.241
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–96（96 aa）	Mutation：N59D	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–96（96 aa）	Mutation：N59D	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–96（96 aa） Chain H 1–96（96 aa）	Mutation：N59D Mutation：N59D	ZN ZINC ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate	Resolution 2.36 Å R-free 0.244
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain Y 1–104（104 aa） Chain d 1–104（104 aa）	Not recorded	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol	Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain i 1–104（104 aa） Chain n 1–104（104 aa）	Not recorded	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol	Resolution 3.82 Å R-free 0.256
6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–96（96 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate	Resolution 2.10 Å R-free 0.249
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain Q 1–657（657 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.90 Å
6T9K SAGA Core module Deposited 2019-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain Q 1–657（657 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.30 Å
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain N 1–657（657 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.60 Å

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SGF73_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–104； UniProt 1–104

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3m99
Deposition date deposition_date	2010-03-21
Structure title title	Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module
Keywords keywords	;Zinc Finger, Activator, Chromatin regulator, Metal-binding, Nucleus, Transcription, Transcription regulation, Zinc-finger, mRNA transport, ubiquitination, deubiquitination, Nuclear pore complex, Protein modification ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.64 Å
Radius of gyration Rg (electron density) rg_electron	27.45 Å
Forward intensity I(0) i0	104021000.00
Molecular weight molecular_weight	79042.0 kDa
Excluded volume excluded_volume	98389 Å³
Envelope volume envelope_volume	123950 Å³
Hydration-shell volume shell_volume	37039 Å³
Envelope diameter envelope_diameter	101.0 Å
Shell Rg shell_rg	35.21 Å
Envelope Rg envelope_rg	27.80 Å
Shape Rg shape_rg	27.39 Å
Total Rg total_rg	28.37 Å
Total atoms total_atoms	5516
Residues n_residues	686
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	94.6 Å
Rg (real space) rg_real	28.57 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	1.0400e+08
I(0) uncertainty (real space) i0_real_error	1.4650e+06
Rg (reciprocal space) rg_reciprocal	28.60 Å
I(0) (reciprocal space) i0_reciprocal	104000000.0000
Solution quality estimate total_estimate	0.8877
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.305
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14360000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 8
Molecular weight formula_weight	53692.3 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5557

MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SAGA-associated factor 11
Molecular weight formula_weight	11297.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDINGLQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Protein SUS1
Molecular weight formula_weight	11094.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	SAGA-associated factor 73
Molecular weight formula_weight	11538.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLENHCAGASGK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3m99c_
Class class	a — All alpha proteins
Fold Fold fold	a.301 — Sus1-like
Superfamily Superfamily superfamily	a.301.1 — Sus1-like
Family Family family	a.301.1.1 — Sus1-like

CATH v4.4 (5 domains)

Domain ID domain_id	3m99A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3m99A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	3m99B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	3m99B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	3m99C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	140 — ENY2/SUS1

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8. Citations (1)

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Unit-cell length a length_a	64.424 Å
Unit-cell length b length_b	103.519 Å
Unit-cell length c length_c	70.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	48.116 Å
R factor r_factor	0.2370
R_work r_work	0.2340
R_free r_free	0.3000

fit	/app/data/saxs_computation/m9/3m99/3m99.fit
pddf	/app/data/pr_computation/m9/3m99/3m99.pr.out
profile	/app/data/saxs_computation/m9/3m99/3m99.dat

Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 8

State in the Current Structure

Other States of the Same Protein in the Database

SAGA-associated factor 11

State in the Current Structure

Other States of the Same Protein in the Database

Protein SUS1

State in the Current Structure

Other States of the Same Protein in the Database

SAGA-associated factor 73

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)