SAXSdb — 2a9u

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–144； UniProt 1–142 Author chain B； PDBConstruct 3–144； 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	2a9u
Deposition date deposition_date	2005-07-12
Structure title title	Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)
Keywords keywords	;coil-coil, Hydrolase, Protease, SH3-binding, Thiol protease, Ubl conjugation pathway, Structural Genomics, Structural Genomics Consortium, SGC ;; HYDROLASE
Experimental Method method	X-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.

2a9u__assembly_1__model_1

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

Download this curve (.dat)

2a9u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2a9u__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.39 Å
Rg (electron density)	24.54 Å
Total Rg	24.96 Å
Atom count	2186
Residues	259
Excluded volume	39160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2a9u__assembly_1__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2a9ua1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.23 — USP8 N-terminal domain-like
Family Family family	a.118.23.1 — USP8 N-terminal domain-like

Domain ID domain_id	d2a9ub_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.23 — USP8 N-terminal domain-like
Family Family family	a.118.23.1 — USP8 N-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	2a9uA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

Domain ID domain_id	2a9uB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

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Unit-cell length a length_a	34.682 Å
Unit-cell length b length_b	64.820 Å
Unit-cell length c length_c	151.895 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	33.810 Å
R factor r_factor	0.2109
R_work r_work	0.2083
R_free r_free	0.2594

Description description	Ubiquitin carboxyl-terminal hydrolase 8
Molecular weight formula_weight	17026.1 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2274

Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2a9u__assembly_1__model_1

2a9u__assembly_1__model_1 | I(q)

2a9u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	88

Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2a9u__assembly_1__model_1

2a9u__assembly_1__model_1 | I(q)

2a9u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)