SAXSdb — 3r42

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

Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Vacuolar protein sorting-associated protein 27 × 1 （P40343） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Vacuolar protein sorting-associated protein 27 × 2 （P40343） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STP22_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–162； UniProt 1–160

Vacuolar protein sorting-associated protein 27

OrganismNot specified

UniProt P40343

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease × 1 （P25604） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease × 2 （P25604） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS27_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–9； UniProt 445–453

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	3r42
Deposition date deposition_date	2011-03-17
Structure title title	Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide
Keywords keywords	endosomal sorting, ESCRT, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

3r42__assembly_1__model_1

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

Download this curve (.dat)

3r42__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3r42__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.74 Å
Rg (electron density)	16.20 Å
Total Rg	17.26 Å
Atom count	1295
Residues	164
Excluded volume	23159 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3r42__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3r42__assembly_2__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	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
Molecular weight formula_weight	18009.5 kDa
Mutation mutation	C133A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1446

GAMSANGKISVPEAVVNWLFKVIQPIYNDGRTTFHDSLALLDNFHSLRPRTRVFTHSDGTPQLLLSIYGTISTGEDGSSPHSIPVIMWVPSMYPVKPPFISINLENFDMNTISSSLPIQEYIDSNGWIALPILHAWDPAAMNLIMVVQELMSLLHEPPQDQA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Vacuolar protein sorting-associated protein 27
Molecular weight formula_weight	1082.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVPSDPYNY

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	151

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3r42a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.2 — UEV domain

CATH v4.4 (1 domains)

Domain ID domain_id	3r42A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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Unit-cell length a length_a	95.200 Å
Unit-cell length b length_b	142.381 Å
Unit-cell length c length_c	32.065 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.866 Å
Low-resolution limit resolution_low	30.973 Å
R factor r_factor	0.1835
R_work r_work	0.1825
R_free r_free	0.2025

Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide

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

Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein 27

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

3r42__assembly_1__model_1

3r42__assembly_1__model_1 | I(q)

3r42__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide

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

Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar protein sorting-associated protein 27

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

3r42__assembly_1__model_1

3r42__assembly_1__model_1 | I(q)

3r42__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)