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3o65

Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative ataxin-3-like protein

Homo sapiens

UniProt Q9H3M9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P0CG47） SODIUM ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P0CG47） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P0CG47） water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P0CG47） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 24 Ubiquitin × 12 （P0CG47） SODIUM ION × 3 water × 15 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 6 Ubiquitin × 3 （P0CG47） SODIUM ION × 1 water × 5 Consistent with protein count
7 Protein homooligomer Homooligomer Protein 12 SODIUM ION × 3 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
3o65

1 assemblies

Heteromeric or nucleic-acid complex
3o65 3o65 3o65 3o65 3o65 3o65

6 assemblies

View Construct and Data Evidence
UniProt name ATX3L_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–191； UniProt 1–190 Author chain C； PDBConstruct 2–191； UniProt 1–190 Author chain E； PDBConstruct 2–191； UniProt 1–190 Author chain G； PDBConstruct 2–191； UniProt 1–190

Ubiquitin

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Putative ataxin-3-like protein × 1 （Q9H3M9） SODIUM ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Putative ataxin-3-like protein × 1 （Q9H3M9） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Putative ataxin-3-like protein × 1 （Q9H3M9） water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Putative ataxin-3-like protein × 1 （Q9H3M9） Consistent with protein count
5 Protein heterocomplex Heteromer Protein 24 Putative ataxin-3-like protein × 12 （Q9H3M9） SODIUM ION × 3 water × 15 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 6 Putative ataxin-3-like protein × 3 （Q9H3M9） SODIUM ION × 1 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2msg 3ons 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4xof 5dk8

32 assemblies; showing the first 12

Homodimer
4zpz 5emz 5emz 5emz 5gob 5goc 5god 5gog 5goh 5goi 5goj 5khy

25 assemblies; showing the first 12

Homotetramer
5go8 5xdp

2 assemblies

Other homooligomers
3zlz 3zlz 3zlz 5go7 5gok 6oq1 6oq1 6oq2 7cap

9 assemblies

Heteromeric or nucleic-acid complex
2mbb 2mro 2n13 2y5b 2y5b 3o65 3o65 3o65 3o65 3o65 3o65 3oj3

362 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76

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_id3o65
Deposition date deposition_date2010-07-28
Structure title titleCrystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity
Keywords keywordsPapain-like fold, Ubiquitin thiolesterase, hydrolase-protein binding complex; hydrolase/protein binding
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3o65__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3o65__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3o65__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.58 Å
Rg (electron density)19.62 Å
Total Rg20.59 Å
Atom count2073
Residues252
Excluded volume37009 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3o65__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3o65__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3o65__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3o65__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3o65__assembly_5__model_1 24-meric （24） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3o65__assembly_6__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 3o65__assembly_7__model_1 dodecameric （12） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3o65b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3o65d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3o65f_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3o65h_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (12 domains)

Domain ID domain_id3o65A01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3o65A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily10 — S15/NS1, RNA-binding
Domain ID domain_id3o65B00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3o65C01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3o65C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily10 — S15/NS1, RNA-binding
Domain ID domain_id3o65D00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3o65E01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3o65E02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily10 — S15/NS1, RNA-binding
Domain ID domain_id3o65F00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3o65G01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3o65G02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily10 — S15/NS1, RNA-binding
Domain ID domain_id3o65H00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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7. Citations (1)