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2i50

Solution Structure of Ubp-M Znf-UBP domain

Method: SOLUTION NMR Dmax: 52.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 16

Homo sapiens

UniProt Q9Y5T5

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 22–143 Fragment：Znf-UBP domain, residues 22-143 ZN ZINC ION × 3 SOLUTION NMR NMR measurement conditions：pH 7；300 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure 1 NMR sample composition：1mM U-15N,13C, 25 mM Sodium Phosphate, 100 mM KCl, 95% H2O, 5% D2O | 95% H2O/5% D2O NMR sample composition：1mM U-15N, 25 mM Sodium Phosphate, 100 mM KCl, 95% H2O, 5% D2O | 95% H2O/5% D2O NMR sample composition：1mM U-15N, 13C, 25 mM Sodium Phosphate, 100 mM KCl, 100% D2O | 100% D2O NMR sample composition：Unlabeled, 25 mM Sodium Phosphate, 100 mM KCl, 100% D2O | 100% D2O Resolution not provided

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 2I50 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 1–823（823 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9YCW Crystal structure of USP16 ZnF-UBP domain Deposited 2025-09-19 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 22–144（123 aa）
Not recorded ZN ZINC ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% (w/v) Glycerol
Resolution 1.80 Å R-free 0.172
9YCW Crystal structure of USP16 ZnF-UBP domain Deposited 2025-09-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–144（123 aa）
Not recorded ZN ZINC ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% (w/v) Glycerol
Resolution 1.80 Å R-free 0.172
9YCW Crystal structure of USP16 ZnF-UBP domain Deposited 2025-09-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 22–144（123 aa）
Not recorded ZN ZINC ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% (w/v) Glycerol
Resolution 1.80 Å R-free 0.172

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBP16_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–126； UniProt 22–143

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 2i50

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2i50
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2i50
Deposition date deposition_date2006-08-23
Structure title titleSolution Structure of Ubp-M Znf-UBP domain
Keywords keywordsALPHA/BETA ZINC-FINGER, RING-FINGER, Znf-UBP, metalloprotein, ubiquitin-binding protein, USP, ubiquitin, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.31 Å
Radius of gyration Rg (electron density) rg_electron14.20 Å
Forward intensity I(0) i01322390000.00
Molecular weight molecular_weight284860.0 kDa
Excluded volume excluded_volume346270 ų
Envelope volume envelope_volume30313 ų
Hydration-shell volume shell_volume15522 ų
Envelope diameter envelope_diameter55.8 Å
Shell Rg shell_rg22.47 Å
Envelope Rg envelope_rg17.12 Å
Shape Rg shape_rg14.20 Å
Total Rg total_rg14.33 Å
Total atoms total_atoms38540
Residues n_residues2440
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 dmax52.0 Å
Rg (real space) rg_real14.30 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.3220e+09
I(0) uncertainty (real space) i0_real_error1.4560e+07
Rg (reciprocal space) rg_reciprocal14.30 Å
I(0) (reciprocal space) i0_reciprocal1322000000.0000
Solution quality estimate total_estimate0.8257
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.1 Å
Skewness Skewness skewness0.373
Kurtosis Kurtosis kurtosis-0.003
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha406100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.596; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.998
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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2i50A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (10)