SAXSdb — 2pjw

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

Uncharacterized protein YHL002W

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 288–375	Non-standard monomer：Yes (specific site not provided by mmCIF)	Vacuolar protein sorting-associated protein 27 × 1 （P40343）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain H； UniProt 288–375	Non-standard monomer：Yes (specific site not provided by mmCIF)	Vacuolar protein sorting-associated protein 27 × 2 （P40343）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	YHA2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–88； UniProt 288–375

Vacuolar protein sorting-associated protein 27

Saccharomyces cerevisiae

UniProt P40343

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain V； UniProt 348–438	Non-standard monomer：Yes (specific site not provided by mmCIF)	Uncharacterized protein YHL002W × 1 （P38753）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain V； UniProt 348–438	Non-standard monomer：Yes (specific site not provided by mmCIF)	Uncharacterized protein YHL002W × 2 （P38753）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.85；288 K；1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 3.01 Å R-free 0.285

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 2PJW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1O06 Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) Deposited 2003-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–320（20 aa） Fragment：Residues 301-320	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.224
1Q0V Solution Structure of Tandem UIMs of Vps27 Deposited 2003-07-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–329（81 aa） Fragment：Tandem UIM	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM Vps27 UIM U-15N \| 90% H2O/10% D2O NMR sample composition 1 mM Vps27 UIM U-15N,U-13C \| 100% D2O	Resolution not provided
1Q0W Solution structure of Vps27 amino-terminal UIM-ubiquitin complex Deposited 2003-07-17	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 256–279（24 aa） Fragment：Amino-terminal UIM, residues 256 to 278	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 100% D2O	Resolution not provided
1VFY PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PROTEIN FROM SACCHAROMYCES CEREVISIAE Deposited 1999-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 163–230（68 aa） Fragment：163-229, FYVE DOMAIN	Mutation：6 RESIDUES (EFIVTD) INSERTED AT C-TERMINUS	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.6, 15% PEG 4000, pH 5.6	Resolution 1.15 Å R-free 0.181
2KDI Solution structure of a Ubiquitin/UIM fusion protein Deposited 2009-01-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 258–277（20 aa） Fragment：UIM 1	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0.103；Pressure ambient NMR sample composition 1.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-100% 15N] Ubiquitin/UIM fusion protein-9, 3 mM sodium azide-10, 20 mM sodium phosphate-11, 50 mM sodium chloride-12, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3R42 Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide Deposited 2011-03-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 445–453（9 aa） Fragment：PSDP peptide (UNP residues 445-453)	Not recorded	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 construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 445–453（9 aa） Fragment：PSDP peptide (UNP residues 445-453)	Not recorded	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
6NJG Ubiquitin Variant in Complex with Ubiquitin Interacting Motif Deposited 2019-01-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 256–278（23 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid	Resolution 2.35 Å R-free 0.244

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS27_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain V； PDBConstruct 1–91； UniProt 348–438

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	2pjw
Deposition date deposition_date	2007-04-16
Structure title title	The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting
Keywords keywords	GAT domain, Core complex, Doamin Swap, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	26.31 Å
Radius of gyration Rg (electron density) rg_electron	26.46 Å
Forward intensity I(0) i0	8442670.00
Molecular weight molecular_weight	20803.0 kDa
Excluded volume excluded_volume	25507 Å³
Envelope volume envelope_volume	32372 Å³
Hydration-shell volume shell_volume	12509 Å³
Envelope diameter envelope_diameter	98.4 Å
Shell Rg shell_rg	28.33 Å
Envelope Rg envelope_rg	27.21 Å
Shape Rg shape_rg	26.49 Å
Total Rg total_rg	26.60 Å
Total atoms total_atoms	1429
Residues n_residues	171
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

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

Maximum dimension Dmax dmax	96.8 Å
Rg (real space) rg_real	26.93 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	8.4430e+06
I(0) uncertainty (real space) i0_real_error	1.5000e+05
Rg (reciprocal space) rg_reciprocal	26.74 Å
I(0) (reciprocal space) i0_reciprocal	8442000.0000
Solution quality estimate total_estimate	0.6545
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.1 Å
Skewness Skewness skewness	0.634
Kurtosis Kurtosis kurtosis	-0.463
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	868800.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.171; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.018; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein YHL002W
Molecular weight formula_weight	10049.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	1458

KEAIVFSQKTTIDQLHNSLNAASKTGNSNEVLQDPHIGDMYGSVTPLRPQVTRMLGKYAKEKEDMLSLRQVLANAERSYNQLMDRAAN

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Vacuolar protein sorting-associated protein 27
Molecular weight formula_weight	10770.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

VDLSDEEKDSIYMFASLVEKMKSRPLNEILEDSKLQNLAQRVFASKARLNYALNDKAQKYNTLIEMNGKISEIMNIYDRLLEQQLQSINLS

来源 Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2pjwH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1940 —

Domain ID domain_id	2pjwV00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1940 —

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8. Citations (2)

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Unit-cell length a length_a	62.400 Å
Unit-cell length b length_b	62.400 Å
Unit-cell length c length_c	94.560 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.010 Å
Low-resolution limit resolution_low	46.920 Å
R factor r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2850

fit	/app/data/saxs_computation/pj/2pjw/2pjw.fit
pddf	/app/data/pr_computation/pj/2pjw/2pjw.pr.out
profile	/app/data/saxs_computation/pj/2pjw/2pjw.dat

The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting

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

Uncharacterized protein YHL002W

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)