SAXSdb — 1use

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

VASODILATOR-STIMULATED PHOSPHOPROTEIN

HOMO SAPIENS

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 335–379	Fragment：TETRAMERISATION DOMAIN, RESIDUES 335-379	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；35% PEG400, 0.2M SODIUM CITRATE, 0.1M TRIS PH8.5, pH 8.50	Resolution 1.30 Å R-free 0.196

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 1USE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EGX SOLUTION STRUCTURE OF THE ENA-VASP HOMOLOGY 1 (EVH1) DOMAIN OF HUMAN VASODILATOR-STIMULATED PHOSPHOPROTEIN (VASP) Deposited 2000-02-17	Different construct 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 1–115（115 aa） Fragment：EVH1 DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 50 mM KCl, 20 mM KH2PO4；Pressure 1 NMR sample composition 1.3 mM VASP EVH1 DOMAIN 15N,13C; buffer containing 20 mM KH2PO4, 50 mM KCl, 0.2 mM Na3N3; samples were used in both 90% H2O,10% D2O and 99.8% D2O 2 mM VASP EVH1 DOMAIN 15N buffer containing 20 mM KH2PO4, 50 mM KCl, 0.2 mM Na3N3;sample were used in 90% H2O,10% D2O \| 90% H2O,10% D2O and 99.8% D2O	Resolution not provided
1USD human VASP tetramerisation domain L352M Deposited 2003-11-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 335–379（45 aa） Fragment：TETRAMERIZATION DOMAIN, RESIDUES 335-379	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；25% PEG MME550, 0.2M NA-CITRATE, 0.1M TRIS PH8.5, pH 8.50	Resolution 1.70 Å R-free 0.224
2PAV Ternary complex of Profilin-Actin with the Last Poly-Pro of Human VASP Deposited 2007-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 199–214（16 aa）	Not recorded	CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277.15 K；200 mM sodium formate, 20% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.80 Å R-free 0.208
2PBD Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP* Deposited 2007-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 203–245（43 aa） Fragment：VASP Loading Poly-Pro Site and GAB domain	Not recorded	CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277.15 K；150mM DL-malic acid pH 7.0, 18% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 1.50 Å R-free 0.190
3CHW Complex of Dictyostelium discoideum Actin with Profilin and the Last Poly-Pro of Human VASP Deposited 2008-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 199–214（16 aa） Fragment：Last Poly-Pro Repeat	Not recorded	CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.1M Bis-Tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.30 Å R-free 0.227
8GAT Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase from A/Indiana/10/2011 (H3N2v), based on consensus cryo-EM map with only Fab 1G01 resolved Deposited 2023-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 337–375（39 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
8GAT Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase from A/Indiana/10/2011 (H3N2v), based on consensus cryo-EM map with only Fab 1G01 resolved Deposited 2023-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 337–375（39 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
8GAT Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase from A/Indiana/10/2011 (H3N2v), based on consensus cryo-EM map with only Fab 1G01 resolved Deposited 2023-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 337–375（39 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
8GAU Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase from A/Indiana/10/2011 (H3N2v) Deposited 2023-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 337–375（39 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.60 Å
8YVL Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab Deposited 2024-03-28	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 Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 337–379（43 aa） Chain B 337–379（43 aa） Chain C 337–379（43 aa） Chain D 337–379（43 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.47 Å
9UAX The structure of Myanmar_N2 and AS4C_Fab complex Deposited 2025-04-01	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 Heteromer；Protein × 12 PDB declaration: 12-meric	Chain I 337–379（43 aa） Chain J 337–379（43 aa） Chain K 337–379（43 aa） Chain L 337–379（43 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9UB1 The structure of Myanmar_N2 and M6B12_Fab complex Deposited 2025-04-02	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 Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 337–379（43 aa） Chain B 337–379（43 aa） Chain C 337–379（43 aa） Chain D 337–379（43 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VASP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–45； UniProt 335–379

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	1use
Deposition date deposition_date	2003-11-21
Structure title title	human VASP tetramerisation domain
Keywords keywords	SIGNALING PROTEIN; SIGNALING 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	17.75 Å
Radius of gyration Rg (electron density) rg_electron	17.77 Å
Forward intensity I(0) i0	524600.00
Molecular weight molecular_weight	4726.0 kDa
Excluded volume excluded_volume	5930 Å³
Envelope volume envelope_volume	8060 Å³
Hydration-shell volume shell_volume	5168 Å³
Envelope diameter envelope_diameter	62.4 Å
Shell Rg shell_rg	18.98 Å
Envelope Rg envelope_rg	18.30 Å
Shape Rg shape_rg	17.76 Å
Total Rg total_rg	18.08 Å
Total atoms total_atoms	333
Residues n_residues	40
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	64.6 Å
Rg (real space) rg_real	18.33 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	5.2460e+05
I(0) uncertainty (real space) i0_real_error	7.7790e+03
Rg (reciprocal space) rg_reciprocal	18.26 Å
I(0) (reciprocal space) i0_reciprocal	524600.0000
Solution quality estimate total_estimate	0.6672
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	9.5 Å
Skewness Skewness skewness	0.624
Kurtosis Kurtosis kurtosis	-0.490
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26060.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.224; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.010; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1usea_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.29 — Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain
Family Family family	h.1.29.1 — Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain

CATH v4.4 (1 domains)

Domain ID domain_id	1useA00
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	1160 — Vasodilator-stimulated phosphoprotein

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8. Citations (1)

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Unit-cell length a length_a	29.701 Å
Unit-cell length b length_b	29.701 Å
Unit-cell length c length_c	100.192 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	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1750
R_work r_work	0.1740
R_free r_free	0.1960

Description description	VASODILATOR-STIMULATED PHOSPHOPROTEIN
Molecular weight formula_weight	5297.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	439

human VASP tetramerisation domain

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

VASODILATOR-STIMULATED PHOSPHOPROTEIN

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

fit	/app/data/saxs_computation/us/1use/1use.fit
pddf	/app/data/pr_computation/us/1use/1use.pr.out
profile	/app/data/saxs_computation/us/1use/1use.dat