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8xpn

The Crystal Structure of USP8 from Biortus.

Method: X-RAY DIFFRACTION Dmax: 115.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 8

Homo sapiens

UniProt P40818

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 734–1110 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 734–1110 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 734–1110 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

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 8XPN 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
8Y9A The Crystal Structure of USP8 from Biortus. Deposited 2024-02-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–142（142 aa）
Not recorded No recorded non-water small molecule 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

8 other PDB entries and 13 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 1–377； UniProt 734–1110 Author chain B； PDBConstruct 1–377； UniProt 734–1110 Author chain C； PDBConstruct 1–377； UniProt 734–1110

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8xpn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8xpn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8xpn
Deposition date deposition_date2024-01-04
最后修订 last_revision2024-03-06
Structure title titleThe Crystal Structure of USP8 from Biortus.
Keywords keywordsHydrolase, Protease, Thiol protease; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.94 Å
Radius of gyration Rg (electron density) rg_electron35.18 Å
Forward intensity I(0) i0212633000.00
Molecular weight molecular_weight116760.0 kDa
Excluded volume excluded_volume145930 ų
Envelope volume envelope_volume198930 ų
Hydration-shell volume shell_volume47711 ų
Envelope diameter envelope_diameter117.5 Å
Shell Rg shell_rg41.56 Å
Envelope Rg envelope_rg34.14 Å
Shape Rg shape_rg35.16 Å
Total Rg total_rg35.73 Å
Total atoms total_atoms8215
Residues n_residues1015
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax115.5 Å
Rg (real space) rg_real35.87 Å
Rg uncertainty (real space) rg_real_error1.00 Å
I(0) (real space) i0_real2.1260e+08
I(0) uncertainty (real space) i0_real_error3.6980e+06
Rg (reciprocal space) rg_reciprocal35.92 Å
I(0) (reciprocal space) i0_reciprocal212600000.0000
Solution quality estimate total_estimate0.9007
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.0 Å
Skewness Skewness skewness0.229
Kurtosis Kurtosis kurtosis-0.562
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19730000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.887
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)