SAXSdb — 3r3q

▼

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–160	Fragment：N-terminal UEV domain (UNP residues 1-160) Mutation：C133A	ZN ZINC ION × 9 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 7 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；0.2 M zinc acetate, 0.1 M imidazole, 25% 1,2-propanediol, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.45 Å R-free 0.184

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3R3Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1UZX A complex of the Vps23 UEV with ubiquitin Deposited 2004-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–161（161 aa） Fragment：UEV DOMAIN, RESIDUES 1-161	Non-standard monomer：Yes (specific site not provided by mmCIF)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22% PEG 8000, 0.1M MES PH 6.5, 0.2M (NH4)2SO4	Resolution 1.85 Å R-free 0.274
2CAZ ESCRT-I core Deposited 2005-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 305–385（81 aa） Fragment：RESIDUES 305-385	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2CAZ ESCRT-I core Deposited 2005-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 305–385（81 aa） Fragment：RESIDUES 305-385	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385)	Mutation：C344A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385)	Mutation：C344A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385) Chain D 322–385（64 aa） Fragment：Vps23C-Terminal Domain (322-385)	Mutation：C344A Mutation：C344A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F6M Structure of a Vps23-C:Vps28-N subcomplex Deposited 2005-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 322–385（64 aa） Fragment：Vps23C-terminal domain (322-385)	Mutation：C344A	MG MAGNESIUM ION × 1 DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261
2F6M Structure of a Vps23-C:Vps28-N subcomplex Deposited 2005-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 322–385（64 aa） Fragment：Vps23C-terminal domain (322-385)	Mutation：C344A	DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 215–385（171 aa） Fragment：Vps23 (215-385)	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–160（160 aa） Fragment：N-terminal UEV domain (UNP residues 1-160)	Mutation：C133A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；288 K；0.2 M sodium phosphate monobasic, 20% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.87 Å R-free 0.203
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–160（160 aa） Fragment：N-terminal UEV domain (UNP residues 1-160)	Mutation：C133A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；288 K；0.2 M sodium phosphate monobasic, 20% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.87 Å R-free 0.203

6 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

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

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3r3q
Deposition date deposition_date	2011-03-16
Structure title title	Crystal structure of the yeast Vps23 UEV domain
Keywords keywords	endosomal sorting, ESCRT-I, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.31 Å
Radius of gyration Rg (electron density) rg_electron	16.60 Å
Forward intensity I(0) i0	6832780.00
Molecular weight molecular_weight	18484.0 kDa
Excluded volume excluded_volume	22813 Å³
Envelope volume envelope_volume	27331 Å³
Hydration-shell volume shell_volume	14335 Å³
Envelope diameter envelope_diameter	62.5 Å
Shell Rg shell_rg	22.17 Å
Envelope Rg envelope_rg	17.19 Å
Shape Rg shape_rg	16.46 Å
Total Rg total_rg	17.98 Å
Total atoms total_atoms	1271
Residues n_residues	153
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	60.8 Å
Rg (real space) rg_real	18.28 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	6.8330e+06
I(0) uncertainty (real space) i0_real_error	8.6530e+04
Rg (reciprocal space) rg_reciprocal	18.28 Å
I(0) (reciprocal space) i0_reciprocal	6833000.0000
Solution quality estimate total_estimate	0.8047
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.217
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	781600.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

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	1427

GAMSANGKISVPEAVVNWLFKVIQPIYNDGRTTFHDSLALLDNFHSLRPRTRVFTHSDGTPQLLLSIYGTISTGEDGSSPHSIPVIMWVPSMYPVKPPFISINLENFDMNTISSSLPIQEYIDSNGWIALPILHAWDPAAMNLIMVVQELMSLLHEPPQDQA

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3r3qa_
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	3r3qA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

▶

8. Citations (1)

▶

Unit-cell length a length_a	36.059 Å
Unit-cell length b length_b	47.139 Å
Unit-cell length c length_c	92.946 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	4

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

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	33.618 Å
R factor r_factor	0.1652
R_work r_work	0.1642
R_free r_free	0.1839

fit	/app/data/saxs_computation/r3/3r3q/3r3q.fit
pddf	/app/data/pr_computation/r3/3r3q/3r3q.pr.out
profile	/app/data/saxs_computation/r3/3r3q/3r3q.dat

Crystal structure of the yeast Vps23 UEV domain