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2aga

De-ubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain

Method: SOLUTION NMR Dmax: 58.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Machado-Joseph disease protein 1

Homo sapiens

UniProt P54252

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 1–185 Fragment：Josephin domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.4；298 K；Ionic strength (raw mmCIF value) 20 mM KPO4；Pressure 1 NMR sample composition：2mM Josephin domain U-15N,13C; 20mM phosphate buffer pH 6.4; 90% H2O, 10% D2O | 90% H2O/10% 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 2AGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1YZB Solution structure of the Josephin domain of Ataxin-3 Deposited 2005-02-28 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–182（182 aa） Fragment：N-terminal domain of Ataxin-3
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM sodium phosphate；Pressure ambient
NMR sample composition 0.4mM of Josephin 15N, 13C; 20mM sodium phosphate buffer (pH 6.5); 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2DOS Structural basis for the recognition of Lys48-linked polyubiquitin chain by the Josephin domain of ataxin-3, a putative deubiquitinating enzyme Deposited 2006-05-03 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–171（171 aa） Fragment：Josephin domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 10mM Sodium phosphate buffer；Pressure 1
NMR sample composition 1.2mM Josephin domain U-15N,13C; 10mM Sodium phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.2mM Josephin domain U-15N,13C; 10mM Sodium phosphate buffer; 99% D2O | 99% D2O
Resolution not provided
2JRI Solution structure of the Josephin domain of Ataxin-3 in complex with ubiquitin molecule. Deposited 2007-06-27 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–182（182 aa） Fragment：N-terminal domain of ataxin-3 sequence database residues 1-182
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 0.1 - 0.3 mM [U-15N] protein, 0.1 -0.3 mM [U-13C; U-15N] protein, 0.1-0.3 mM protein, 0.1-0.3 mM [U-13C; U-15N; U-2H] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KLZ Solution Structure of the Tandem UIM Domain of Ataxin-3 Complexed with Ubiquitin Deposited 2009-07-12 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 222–263（42 aa） Fragment：UIM1 and UIM 2 domain, UNP residues 222-263
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] protein-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 0.02 % sodium azide-4, 4 mM ubiquitin-5, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein-6, 20 mM sodium phosphate-7, 100 mM sodium chloride-8, 0.02 % sodium azide-9, 4 mM ubiquitin-10, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4WTH Ataxin-3 Carboxy Terminal Region - Crystal C2 (triclinic) Deposited 2014-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 278–324（47 aa） Fragment：MBP residues 27-392 (UNP) + Ataxin-3 C-terminal region (UNP residues 278-324)
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；24% PEG5000 MME, 0.9 M sodium acetate, 0.06 M imidazole, pH 8.0, 0.1 M zinc acetate
Resolution 2.25 Å R-free 0.250
4WTH Ataxin-3 Carboxy Terminal Region - Crystal C2 (triclinic) Deposited 2014-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 278–324（47 aa） Fragment：MBP residues 27-392 (UNP) + Ataxin-3 C-terminal region (UNP residues 278-324)
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；24% PEG5000 MME, 0.9 M sodium acetate, 0.06 M imidazole, pH 8.0, 0.1 M zinc acetate
Resolution 2.25 Å R-free 0.250
4YS9 Ataxin-3 Carboxy-Terminal Region - Crystal C1 (tetragonal) Deposited 2015-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 278–324（47 aa） Fragment：MBP residues 27-392 (UNP) + Ataxin-3 C-terminal region (UNP residues 278-324)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；25% PEG5000 MME, 1.0 M sodium acetate, 0.1 M imidazole, pH 8.0, 0.1 M zinc acetate
Resolution 2.00 Å R-free 0.223

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MJD1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–190； UniProt 1–185

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 2aga

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2aga
Deposition date deposition_date2005-07-26
Structure title titleDe-ubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain
Keywords keywordsPolyglutamine, ubiquitin, UIM, ataxia, VCP/p97, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.17 Å
Radius of gyration Rg (electron density) rg_electron16.71 Å
Forward intensity I(0) i02624450000.00
Molecular weight molecular_weight435470.0 kDa
Excluded volume excluded_volume543620 ų
Envelope volume envelope_volume46753 ų
Hydration-shell volume shell_volume20259 ų
Envelope diameter envelope_diameter65.8 Å
Shell Rg shell_rg26.31 Å
Envelope Rg envelope_rg20.08 Å
Shape Rg shape_rg16.67 Å
Total Rg total_rg16.97 Å
Total atoms total_atoms60340
Residues n_residues3800
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 dmax58.9 Å
Rg (real space) rg_real17.13 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real2.6240e+09
I(0) uncertainty (real space) i0_real_error2.8970e+07
Rg (reciprocal space) rg_reciprocal17.14 Å
I(0) (reciprocal space) i0_reciprocal2624000000.0000
Solution quality estimate total_estimate0.7839
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.9 Å
Skewness Skewness skewness0.315
Kurtosis Kurtosis kurtosis-0.116
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha921200.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.733; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2agaA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily40 —
Domain ID domain_id2agaA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily10 — S15/NS1, RNA-binding
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8. Citations (1)

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9. Files and Curves (10)