SAXSdb — 2qiy

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

UBP3-associated protein BRE5

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ubiquitin carboxyl-terminal hydrolase 3 × 2 （Q01477） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRE5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–152； UniProt 1–146 Author chain B； PDBConstruct 7–152； UniProt 1–146

Ubiquitin carboxyl-terminal hydrolase 3

Saccharomyces cerevisiae

UniProt Q01477

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	UBP3-associated protein BRE5 × 2 （P53741） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBP3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–48； UniProt 190–233 Author chain D； PDBConstruct 5–48； UniProt 190–233

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	2qiy
Deposition date deposition_date	2007-07-05
Structure title title	yeast Deubiquitinase Ubp3 and Bre5 cofactor complex
Keywords keywords	;deubiquitylation, ubiquitin-specific processing proteases(UBPs), NTF2, protein-protein recognition, Hydrolase, Thiol protease, Ubl conjugation pathway, Phosphorylation, RNA-binding, Signaling protein-hydrolase COMPLEX ;; Signaling protein/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.

2qiy__assembly_1__model_1

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

Download this curve (.dat)

2qiy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qiy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.62 Å
Rg (electron density)	19.40 Å
Total Rg	20.36 Å
Atom count	2580
Residues	317
Excluded volume	46299 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qiy__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	UBP3-associated protein BRE5
Molecular weight formula_weight	17675.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2800

GSHMASMGVTVQDICFAFLQNYYERMRTDPSKLAYFYASTAELTHTNYQSKSTNEKDDVLPTVKVTGRENINKFFSRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTGTPVYKFCQTFILLPSSNGSTFDITNDIIRFISNSFKLE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 3
Molecular weight formula_weight	5274.0 kDa
EC 编号 ec_number	3.1.2.15
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GSASVTKLKNLKENSSNLIQLPLFINTTEAEFAAASVQRYELNMKALN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	220

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qiya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.2 — NTF2-like

Domain ID domain_id	d2qiyb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.2 — NTF2-like

CATH v4.4 (2 domains)

Domain ID domain_id	2qiyA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2qiyB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	59.100 Å
Unit-cell length b length_b	90.240 Å
Unit-cell length c length_c	101.480 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	1.690 Å
Low-resolution limit resolution_low	49.450 Å
R factor r_factor	0.2084
R_work r_work	0.2066
R_free r_free	0.2246

yeast Deubiquitinase Ubp3 and Bre5 cofactor complex

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

UBP3-associated protein BRE5

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin carboxyl-terminal hydrolase 3

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

2qiy__assembly_1__model_1

2qiy__assembly_1__model_1 | I(q)

2qiy__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

yeast Deubiquitinase Ubp3 and Bre5 cofactor complex

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

UBP3-associated protein BRE5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin carboxyl-terminal hydrolase 3

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

2qiy__assembly_1__model_1

2qiy__assembly_1__model_1 | I(q)

2qiy__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)