SAXSdb — 1vfy

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

PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF PROTEIN VPS27

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 163–230	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

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 1VFY	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 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 ligand/ion 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 oligomeric state Different ligand/ion 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
2KDI Solution structure of a Ubiquitin/UIM fusion protein Deposited 2009-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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
2PJW The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting Deposited 2007-04-16	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 V 348–438（91 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	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
2PJW The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting Deposited 2007-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 348–438（91 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	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
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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS27_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–68； UniProt 163–230

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	1vfy
Deposition date deposition_date	1999-04-26
Structure title title	PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PROTEIN FROM SACCHAROMYCES CEREVISIAE
Keywords keywords	FYVE DOMAIN, ENDOSOME MATURATION, INTRACELLULAR TRAFFICKING, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	12.92 Å
Radius of gyration Rg (electron density) rg_electron	12.36 Å
Forward intensity I(0) i0	1537170.00
Molecular weight molecular_weight	7770.0 kDa
Excluded volume excluded_volume	9412 Å³
Envelope volume envelope_volume	10756 Å³
Hydration-shell volume shell_volume	7996 Å³
Envelope diameter envelope_diameter	46.7 Å
Shell Rg shell_rg	17.08 Å
Envelope Rg envelope_rg	12.89 Å
Shape Rg shape_rg	12.43 Å
Total Rg total_rg	13.32 Å
Total atoms total_atoms	534
Residues n_residues	67
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	47.8 Å
Rg (real space) rg_real	12.96 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	1.5370e+06
I(0) uncertainty (real space) i0_real_error	1.6430e+04
Rg (reciprocal space) rg_reciprocal	12.96 Å
I(0) (reciprocal space) i0_reciprocal	1537000.0000
Solution quality estimate total_estimate	0.8177
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.5 Å
Skewness Skewness skewness	0.465
Kurtosis Kurtosis kurtosis	-0.049
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	221500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.615; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.978

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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	PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF PROTEIN VPS27
Molecular weight formula_weight	8271.3 kDa
Mutation mutation	6 RESIDUES (EFIVTD) INSERTED AT C-TERMINUS
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	643

DSKTPADWIDSDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNSIPLPDLGIYEPVRVCDSCFEDYEFIVTD

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 BL21(DE3)

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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vfya1
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.1 — FYVE, a phosphatidylinositol-3-phosphate binding domain

Domain ID domain_id	d1vfya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1vfyA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Unit-cell length a length_a	24.090 Å
Unit-cell length b length_b	26.570 Å
Unit-cell length c length_c	31.610 Å
Unit-cell angle α angle_alpha	111.79 °
Unit-cell angle β angle_beta	92.70 °
Unit-cell angle γ angle_gamma	105.70 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	1.150 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1740
R_free r_free	0.1810

fit	/app/data/saxs_computation/vf/1vfy/1vfy.fit
pddf	/app/data/pr_computation/vf/1vfy/1vfy.pr.out
profile	/app/data/saxs_computation/vf/1vfy/1vfy.dat

PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PROTEIN FROM SACCHAROMYCES CEREVISIAE

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

PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF PROTEIN VPS27

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