SAXSdb — 4w4u

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

Ubiquitin carboxyl-terminal hydrolase

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	Transcription and mRNA export factor SUS1 × 1 （N1P8F5） SAGA-associated factor 11 × 1 （N1NXA6） SAGA-associated factor 73 × 1 （P53165） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–471	Not recorded	Transcription and mRNA export factor SUS1 × 1 （N1P8F5） SAGA-associated factor 11 × 1 （N1NXA6） SAGA-associated factor 73 × 1 （P53165） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	N1P0J5_YEASC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–476； UniProt 1–471 Author chain D； PDBConstruct 6–476； UniProt 1–471

Transcription and mRNA export factor SUS1

Saccharomyces cerevisiae

UniProt N1P8F5

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 1–96	Not recorded	Ubiquitin carboxyl-terminal hydrolase × 1 （N1P0J5） SAGA-associated factor 11 × 1 （N1NXA6） SAGA-associated factor 73 × 1 （P53165） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 1–96	Not recorded	Ubiquitin carboxyl-terminal hydrolase × 1 （N1P0J5） SAGA-associated factor 11 × 1 （N1NXA6） SAGA-associated factor 73 × 1 （P53165） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	N1P8F5_YEASC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–96； UniProt 1–96 Author chain F； PDBConstruct 1–96； UniProt 1–96

SAGA-associated factor 11

Saccharomyces cerevisiae

UniProt N1NXA6

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 1–99	Not recorded	Ubiquitin carboxyl-terminal hydrolase × 1 （N1P0J5） Transcription and mRNA export factor SUS1 × 1 （N1P8F5） SAGA-associated factor 73 × 1 （P53165） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain G； UniProt 1–99	Not recorded	Ubiquitin carboxyl-terminal hydrolase × 1 （N1P0J5） Transcription and mRNA export factor SUS1 × 1 （N1P8F5） SAGA-associated factor 73 × 1 （P53165） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	N1NXA6_YEASC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–99； UniProt 1–99 Author chain G； PDBConstruct 1–99； UniProt 1–99

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 E； UniProt 1–96	Mutation：Y57A	Ubiquitin carboxyl-terminal hydrolase × 1 （N1P0J5） Transcription and mRNA export factor SUS1 × 1 （N1P8F5） SAGA-associated factor 11 × 1 （N1NXA6） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain H； UniProt 1–96	Mutation：Y57A	Ubiquitin carboxyl-terminal hydrolase × 1 （N1P0J5） Transcription and mRNA export factor SUS1 × 1 （N1P8F5） SAGA-associated factor 11 × 1 （N1NXA6） 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

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 4W4U	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 mutation/modification 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
3M99 Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module Deposited 2010-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–104（104 aa） Fragment：UNP RESIDUES: 1-104	Not recorded	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
3MHH Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module Deposited 2010-04-08	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） 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 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 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 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） 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
4WA6 Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution Deposited 2014-08-28	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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 16 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 E； PDBConstruct 1–96； UniProt 1–96 Author chain H； PDBConstruct 1–96； UniProt 1–96

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	4w4u
Deposition date deposition_date	2014-08-15
Structure title title	Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution
Keywords keywords	Multi-Protein Complex, Hydrolase-transcription complex, transcription-hydrolase complex; transcription/hydrolase
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	43.12 Å
Radius of gyration Rg (electron density) rg_electron	42.96 Å
Forward intensity I(0) i0	343933000.00
Molecular weight molecular_weight	150450.0 kDa
Excluded volume excluded_volume	187640 Å³
Envelope volume envelope_volume	254580 Å³
Hydration-shell volume shell_volume	51205 Å³
Envelope diameter envelope_diameter	155.1 Å
Shell Rg shell_rg	45.23 Å
Envelope Rg envelope_rg	42.81 Å
Shape Rg shape_rg	42.91 Å
Total Rg total_rg	43.27 Å
Total atoms total_atoms	10497
Residues n_residues	1309
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	147.8 Å
Rg (real space) rg_real	43.45 Å
Rg uncertainty (real space) rg_real_error	1.99 Å
I(0) (real space) i0_real	3.4390e+08
I(0) uncertainty (real space) i0_real_error	7.3400e+06
Rg (reciprocal space) rg_reciprocal	43.12 Å
I(0) (reciprocal space) i0_reciprocal	343800000.0000
Solution quality estimate total_estimate	0.8339
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.0 Å
Skewness Skewness skewness	0.491
Kurtosis Kurtosis kurtosis	-0.454
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58590000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.848; Smooth: 0.744

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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
Molecular weight formula_weight	54033.6 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	10594

GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	889517
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Transcription and mRNA export factor SUS1
Molecular weight formula_weight	11094.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	889517
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	SAGA-associated factor 11
Molecular weight formula_weight	11297.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDINGLQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	889517
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	SAGA-associated factor 73
Molecular weight formula_weight	10732.2 kDa
Mutation mutation	Y57A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,H

MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKAFNPNAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
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	13

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4w4ub_
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

Domain ID domain_id	d4w4uf_
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 (7 domains)

Domain ID domain_id	4w4uA01
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	4w4uA02
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	4w4uB00
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

Domain ID domain_id	4w4uD01
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	4w4uD02
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	4w4uF00
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

Domain ID domain_id	4w4uG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

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8. Citations (1)

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Unit-cell length a length_a	80.739 Å
Unit-cell length b length_b	67.273 Å
Unit-cell length c length_c	137.145 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.020 Å
R factor r_factor	0.1850
R_work r_work	0.1820
R_free r_free	0.2407

fit	/app/data/saxs_computation/w4/4w4u/4w4u.fit
pddf	/app/data/pr_computation/w4/4w4u/4w4u.pr.out
profile	/app/data/saxs_computation/w4/4w4u/4w4u.dat

Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution

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

Ubiquitin carboxyl-terminal hydrolase

State in the Current Structure

Other States of the Same Protein in the Database

Transcription and mRNA export factor SUS1

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

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) 9 domains

SCOP 2.08 (2 domains)

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)