SAXSdb — 8y9a

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

Ubiquitin carboxyl-terminal hydrolase 8

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–142	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；4.0M Na formate	Resolution 3.10 Å R-free 0.268

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 8Y9A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WHB Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8 (UBP8) Deposited 2004-05-28	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 176–319（144 aa） Fragment：Rhodanese-like domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM protein, 20mM d-Tris-HCl, pH 7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2A9U Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8) Deposited 2005-07-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Fragment：N-terminal domain, residues 1-142 Chain B 1–142（142 aa） Fragment：N-terminal domain, residues 1-142	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；27% PEG3350, 0.2 M Li2SO4, 0.1 M bisTris, pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298 K	Resolution 2.10 Å R-free 0.259
2GFO Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8 Deposited 2006-03-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 734–1110（377 aa） Fragment：Catalytic Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；18% PEG3350; 0.1 M bis-Tris, pH 6.3, 0.2 M KSCN, 1 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 298, temperature 298.0K	Resolution 2.00 Å R-free 0.210
2GWF Structure of a USP8-NRDP1 complex Deposited 2006-05-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 181–318（138 aa） Fragment：Rhodanase domain, residues 181-318	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.30 Å R-free 0.237
2GWF Structure of a USP8-NRDP1 complex Deposited 2006-05-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 181–318（138 aa） Fragment：Rhodanase domain, residues 181-318	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.30 Å R-free 0.237
2GWF Structure of a USP8-NRDP1 complex Deposited 2006-05-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 181–318（138 aa） Fragment：Rhodanase domain, residues 181-318	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.30 Å R-free 0.237
3N3K The catalytic domain of USP8 in complex with a USP8 specific inhibitor Deposited 2010-05-20	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 A 734–1110（377 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；24% PEG3350, 0.1 M BIS-TRIS, 0.2 M AMMONIUM ACETATE, 1 MM DTT, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.242
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 712–724（13 aa） Chain D 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 712–724（13 aa） Chain C 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 712–724（13 aa） Chain D 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
6F09 Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 712–724（13 aa） Chain C 712–724（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M phosphate citrate pH 4.4; 40% PEG 300	Resolution 1.59 Å R-free 0.225
8ADM Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and small molecule stabilizer Deposited 2022-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 715–722（8 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	O6C 1-[2-(4-chloranylphenoxy)-2-methyl-propanoyl]-~{N}-[2-[2-(dimethylamino)ethyldisulfanyl]ethyl]piperidine-4-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer system 1 (Imidazole; MES monohydrate) pH 6.5 and 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)	Resolution 1.70 Å R-free 0.222
8XPN The Crystal Structure of USP8 from Biortus. Deposited 2024-01-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 734–1110（377 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9	Resolution 2.10 Å R-free 0.216
8XPN The Crystal Structure of USP8 from Biortus. Deposited 2024-01-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 734–1110（377 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9	Resolution 2.10 Å R-free 0.216
8XPN The Crystal Structure of USP8 from Biortus. Deposited 2024-01-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 734–1110（377 aa）	Not recorded	ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9	Resolution 2.10 Å R-free 0.216

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

View Construct and Data Evidence

UniProt name	UBP8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–142； UniProt 1–142

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	8y9a
Deposition date deposition_date	2024-02-06
最后修订 last_revision	2024-03-06
Structure title title	The Crystal Structure of USP8 from Biortus.
Keywords keywords	Hydrolase, Protease, Thiol protease, Cell cycle, Ubl conjugation pathway; 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	22.03 Å
Radius of gyration Rg (electron density) rg_electron	21.59 Å
Forward intensity I(0) i0	4258360.00
Molecular weight molecular_weight	15047.0 kDa
Excluded volume excluded_volume	18989 Å³
Envelope volume envelope_volume	26379 Å³
Hydration-shell volume shell_volume	12101 Å³
Envelope diameter envelope_diameter	83.5 Å
Shell Rg shell_rg	24.49 Å
Envelope Rg envelope_rg	22.64 Å
Shape Rg shape_rg	21.59 Å
Total Rg total_rg	22.13 Å
Total atoms total_atoms	1060
Residues n_residues	127
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	82.9 Å
Rg (real space) rg_real	22.51 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	4.2580e+06
I(0) uncertainty (real space) i0_real_error	6.5720e+04
Rg (reciprocal space) rg_reciprocal	22.42 Å
I(0) (reciprocal space) i0_reciprocal	4258000.0000
Solution quality estimate total_estimate	0.7571
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.674
Kurtosis Kurtosis kurtosis	-0.037
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	436700.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.561; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.174; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	103.008 Å
Unit-cell length b length_b	103.008 Å
Unit-cell length c length_c	93.254 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	40.240 Å
R factor r_factor	—
R_work r_work	0.1979
R_free r_free	0.2681

Description description	Ubiquitin carboxyl-terminal hydrolase 8
Molecular weight formula_weight	16788.2 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1089

The Crystal Structure of USP8 from Biortus.

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

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

fit	/app/data/saxs_computation/y9/8y9a/8y9a.fit
pddf	/app/data/pr_computation/y9/8y9a/8y9a.pr.out
profile	/app/data/saxs_computation/y9/8y9a/8y9a.dat