6dj9

Structure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 15

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
4	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP15_HUMAN
Isoform	Q9Y4E8-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–138； UniProt 1–134 Author chain B； PDBConstruct 5–138； UniProt 1–134 Author chain C； PDBConstruct 5–138； UniProt 1–134 Author chain D； PDBConstruct 5–138； UniProt 1–134 Author chain E； PDBConstruct 5–138； UniProt 1–134 Author chain F； PDBConstruct 5–138； UniProt 1–134

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	6dj9
Deposition date deposition_date	2018-05-24
Structure title title	Structure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV)
Keywords keywords	deubiquitination, Ubv, high-affinity, strand-exchange, dimerization, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

6dj9__assembly_1__model_1

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

Download this curve (.dat)

6dj9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6dj9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.88 Å
Rg (electron density)	18.83 Å
Total Rg	19.71 Å
Atom count	1213
Residues	155
Excluded volume	21638 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6dj9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6dj9__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6dj9__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6dj9__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6dj9__assembly_5__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6dj9__assembly_6__model_1`	hexameric （6）	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)

Entity 1 Entity 1 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 15
Molecular weight formula_weight	15987.0 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9759

GAAAMAEGGAADLDTQRSDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTSSG

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin Variant UbV 15.D
Molecular weight formula_weight	9513.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

GAGMQIFVSTAWFCGKLITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESGLQLHRRLRPTSGSSG

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6dj9a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

Domain ID domain_id	d6dj9b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

Domain ID domain_id	d6dj9c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

Domain ID domain_id	d6dj9d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

Domain ID domain_id	d6dj9e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

Domain ID domain_id	d6dj9f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.324 — DUSP-like
Superfamily Superfamily superfamily	d.324.1 — DUSP-like
Family Family family	d.324.1.1 — DUSP, domain in ubiquitin-specific proteases

Domain ID domain_id	d6dj9g_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6dj9h_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6dj9i_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6dj9j_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6dj9k_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6dj9l_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (4 domains)

Domain ID domain_id	6dj9A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

Domain ID domain_id	6dj9C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

Domain ID domain_id	6dj9D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

Domain ID domain_id	6dj9E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2230 — DUSP-like
Homologous superfamily homologous superfamily	10 — DUSP-like

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Unit-cell length a length_a	152.410 Å
Unit-cell length b length_b	152.410 Å
Unit-cell length c length_c	125.461 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	90.935 Å
R factor r_factor	0.2548
R_work r_work	0.2533
R_free r_free	0.2672

Structure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 15

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

6dj9__assembly_1__model_1

6dj9__assembly_1__model_1 | I(q)

6dj9__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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (12 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 15

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

6dj9__assembly_1__model_1

6dj9__assembly_1__model_1 | I(q)

6dj9__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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (12 domains)

CATH v4.4 (4 domains)

7. Citations (1)