SAXSdb — 1u6h

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

Vinculin

Gallus gallus

UniProt P12003

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 A； UniProt 0–258	Fragment：Residues 0-258	Talin × 1 （Q8AWI0）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 8000, Tris-HCl, magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.38 Å R-free 0.322

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 1U6H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QKR Crystal structure of the vinculin tail and a pathway for activation Deposited 1999-08-04	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 878–1065（188 aa） Fragment：C-TERMINAL DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；25% (W/V) PEG 2000, 0.2 M (NH4)2SO4, 0.1 M CH3COO PH 5.0	Resolution 1.80 Å R-free 0.248
1QKR Crystal structure of the vinculin tail and a pathway for activation Deposited 1999-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 878–1065（188 aa） Fragment：C-TERMINAL DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；25% (W/V) PEG 2000, 0.2 M (NH4)2SO4, 0.1 M CH3COO PH 5.0	Resolution 1.80 Å R-free 0.248
1ST6 Crystal structure of a cytoskeletal protein Deposited 2004-03-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1065（1065 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；ammonium sulphate, cacodylic acid, dtt, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K	Resolution 3.10 Å R-free 0.357
1T01 Vinculin complexed with the VBS1 helix from talin Deposited 2004-04-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa） Fragment：vinculin head	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；30%PEG 5000, 0.1M MES, 0.2M Ammonium Sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50	Resolution 2.06 Å R-free 0.303
1XWJ Vinculin head (1-258) in complex with the talin vinculin binding site 3 (1945-1969) Deposited 2004-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa） Fragment：residues -21-258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1M NaH2PO4, 1M K2HPO4, 0.1M CAPS, pH 10.9, 3% Hexanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.281
1ZVZ Vinculin Head (0-258) in Complex with the Talin Rod Residue 820-844 Deposited 2005-06-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa） Fragment：Residues 0-258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.276
1ZW2 Vinculin Head (0-258) in Complex with the Talin Rod residues 2345-2369 Deposited 2005-06-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM Tris, pH 7.0, 20% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.295
1ZW3 Vinculin Head (0-258) in Complex with the Talin Rod residues 1630-1652 Deposited 2005-06-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–258（258 aa） Fragment：Residues 0-258	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；1.2M NaH2PO4/0.8M K2HPO4, 100mM CAPS, pH 10.5, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.307
2GDC Structure of Vinculin VD1 / IpaA560-633 complex Deposited 2006-03-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–265（265 aa） Fragment：VD1 domain (RESIDUES 0-265)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES, 10% 2-propanol, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.74 Å R-free 0.294
3JBI MDFF model of the vinculin tail domain bound to F-actin Deposited 2015-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 879–1130（252 aa） Fragment：tail domain (UNP residues 879-1130)	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole；pH 7；50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole cryo-EM vitrification conditions 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of Vt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging.；Cryogen ETHANE；3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of Vt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging into liquid ethane (LEICA EM GP).	Resolution 8.50 Å
3ZDL Vinculin head (1-258) in complex with a RIAM fragment Deposited 2012-11-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa） Fragment：VD1 DOMAIN, RESIDUES 1-259	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 1.2M AMMONIUM SULPHATE, 0.05M TRI-SODIUM CITRATE, 3% ISOPROPANOL	Resolution 2.30 Å R-free 0.230
4E17 Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin Deposited 2012-03-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa） Fragment：D1 domain (UNP residues 1-259)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；283 K；20% PEG8000, 100 mM MES, pH 6.8, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.30 Å R-free 0.240
4E18 Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin Deposited 2012-03-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa） Fragment：D1 domain (UNP residues 1-259)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；22% PEG3350, 100 mM bis-tris-propane, pH 8.0, 100 mM sodium nitrate, 3 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.273
6FQ4 Structure of Chlamydial virulence factor TarP and vinculin head domain Deposited 2018-02-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1 M sodium citrate tribasic dehydrate pH 5.6, 20% 2-propanol	Resolution 2.89 Å R-free 0.346
6NR7 Rerefinement of chicken vinculin Deposited 2019-01-23	Different construct 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 1–1066（1066 aa）	Not recorded	SO4 SULFATE ION × 2 KYG (1R,2R,3S,4R,5R,6S)-4-{[(S)-[(2S)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-3,5,6-trihydroxycyclohexane-1,2-diyl bis[dihydrogen (phosphate)] × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；303 K；ammonium sulphate, cacodylic acid, dtt, pH 6.5	Resolution 3.00 Å R-free 0.315

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VINC_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–280； UniProt 0–258

Talin

OrganismNot specified

UniProt Q8AWI0

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 B； UniProt 849–879	Fragment：Vinculin Binding Site 2 (residues 849-879)	Vinculin × 1 （P12003）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 8000, Tris-HCl, magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.38 Å R-free 0.322

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 1U6H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XWJ Vinculin head (1-258) in complex with the talin vinculin binding site 3 (1945-1969) Deposited 2004-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1944–1969（26 aa） Fragment：residues 1945-1970	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1M NaH2PO4, 1M K2HPO4, 0.1M CAPS, pH 10.9, 3% Hexanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.281

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8AWI0_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–31； UniProt 849–879

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	1u6h
Deposition date deposition_date	2004-07-30
Structure title title	Vinculin head (0-258) in complex with the talin vinculin binding site 2 (849-879)
Keywords keywords	Protein-protein complex, cell adhesion; CELL ADHESION
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	26.28 Å
Radius of gyration Rg (electron density) rg_electron	26.43 Å
Forward intensity I(0) i0	15483400.00
Molecular weight molecular_weight	30273.0 kDa
Excluded volume excluded_volume	38191 Å³
Envelope volume envelope_volume	47182 Å³
Hydration-shell volume shell_volume	17572 Å³
Envelope diameter envelope_diameter	102.8 Å
Shell Rg shell_rg	28.84 Å
Envelope Rg envelope_rg	26.77 Å
Shape Rg shape_rg	26.46 Å
Total Rg total_rg	26.65 Å
Total atoms total_atoms	2115
Residues n_residues	276
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	98.9 Å
Rg (real space) rg_real	26.81 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	1.5480e+07
I(0) uncertainty (real space) i0_real_error	2.5580e+05
Rg (reciprocal space) rg_reciprocal	26.64 Å
I(0) (reciprocal space) i0_reciprocal	15480000.0000
Solution quality estimate total_estimate	0.7206
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.727
Kurtosis Kurtosis kurtosis	-0.024
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3593000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.415; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.145; Smooth: 0.973

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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	Vinculin
Molecular weight formula_weight	31327.1 kDa
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	2172

MGSSHHHHHHSSGLVPRGSHMMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVSAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVRAAQMLQADPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKSQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAWA

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Talin
Molecular weight formula_weight	3133.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DLENSRKLLSAAKILADATAKMVEAAKGAAA

Entity 3 Entity 3 water

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

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1u6hA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	1u6hA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

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8. Citations (1)

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Unit-cell length a length_a	52.122 Å
Unit-cell length b length_b	69.154 Å
Unit-cell length c length_c	96.162 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2457
R_work r_work	0.2420
R_free r_free	0.3223

fit	/app/data/saxs_computation/u6/1u6h/1u6h.fit
pddf	/app/data/pr_computation/u6/1u6h/1u6h.pr.out
profile	/app/data/saxs_computation/u6/1u6h/1u6h.dat

Vinculin head (0-258) in complex with the talin vinculin binding site 2 (849-879)

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

Vinculin

State in the Current Structure

Other States of the Same Protein in the Database

Talin

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

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)