← Back to search
6fuy

Crystal structure of human full-length vinculin-T12-A974K (residues 1-1066)

Method: X-RAY DIFFRACTION Dmax: 111.1 Å Quality: GOOD
▼

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

Vinculin

Homo sapiens

UniProt P18206

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 1–1066 Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277.15 K；PEG 4000, calcium acetate, Tris-HOAc, 15% ethylene glycol Resolution 3.00 Å R-free 0.305

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 6FUY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RKC Human vinculin head (1-258) in complex with talin's vinculin binding site 3 (residues 1944-1969) Deposited 2003-11-21 Different construct 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 1–258（258 aa） Fragment：vinculin head (residues 1-258)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；293 K；2% MPD; 100 mM citric acid (pH 4); 100 mM CdCl2, pH 4.0, temperature 293K
Resolution 2.70 Å R-free 0.335
1RKE Human vinculin head (1-258) in complex with human vinculin tail (879-1066) Deposited 2003-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–258（258 aa） Fragment：vinculin head (residues 1-258)
Chain B 882–1066（185 aa） Fragment：vinculin tail (residues 879-1066)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；293 K；15% PEG 3350; 50 mM NaCl; 100 mM Tris (pH 8); 10 mM DTT, pH 8.0, temperature 293K
Resolution 2.35 Å R-free 0.278
1SYQ Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin binding site 1, residues 607-636 Deposited 2004-04-01 Different construct 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 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.42 Å R-free 0.236
1SYQ Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin binding site 1, residues 607-636 Deposited 2004-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.42 Å R-free 0.236
1SYQ Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin binding site 1, residues 607-636 Deposited 2004-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–258（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.42 Å R-free 0.236
1TR2 Crystal structure of human full-length vinculin (residues 1-1066) Deposited 2004-06-19 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 0–1065（1066 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å R-free 0.300
1TR2 Crystal structure of human full-length vinculin (residues 1-1066) Deposited 2004-06-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 0–1065（1066 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å R-free 0.300
2GWW Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site (residues 602-633) Deposited 2006-05-07 Different construct 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 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.72 Å R-free 0.291
2GWW Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site (residues 602-633) Deposited 2006-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.72 Å R-free 0.291
2GWW Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site (residues 602-633) Deposited 2006-05-07 Different construct 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 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.72 Å R-free 0.291
2HSQ Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site 2 (residues 565-587) Deposited 2006-07-22 Different construct 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 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.97 Å R-free 0.316
2HSQ Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site 2 (residues 565-587) Deposited 2006-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain A 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.97 Å R-free 0.316
2HSQ Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site 2 (residues 565-587) Deposited 2006-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.97 Å R-free 0.316
2IBF Human vinculin's head domain (Vh1, residues 1-258) in complex with two vinculin binding sites of Shigella flexneri's IpaA (residues 565-587) Deposited 2006-09-11 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 A 0–257（258 aa） Fragment：Head domain (Vh1): Residues 1-258
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.270
3JBK Cryo-EM reconstruction of the metavinculin-actin interface Deposited 2015-09-03 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 M 858–1129（272 aa） Fragment：tail domain (UNP residues 858-1129)
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 MVt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of MVt 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 MVt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of MVt 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 8.20 Å
3MYI Human metavinculin tail domain Deposited 2010-05-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 959–1130（172 aa） Fragment：UNP residues 959-1134
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.247
3RF3 Shigella IpaA-VBS3 in complex with human vinculin Deposited 2011-04-05 Different construct 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 1–258（258 aa） Fragment：unp residues 1-258
Not recorded CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K
Resolution 1.61 Å R-free 0.195
3RF3 Shigella IpaA-VBS3 in complex with human vinculin Deposited 2011-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–258（258 aa） Fragment：unp residues 1-258
Not recorded CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K
Resolution 1.61 Å R-free 0.195
3RF3 Shigella IpaA-VBS3 in complex with human vinculin Deposited 2011-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–258（258 aa） Fragment：unp residues 1-258
Chain B 1–258（258 aa） Fragment：unp residues 1-258
Not recorded CAC CACODYLATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K
Resolution 1.61 Å R-free 0.195
3S90 Human vinculin head domain Vh1 (residues 1-252) in complex with murine talin (VBS33; residues 1512-1546) Deposited 2011-05-31 Different construct 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 1–252（252 aa） Fragment：unp residues 1-252
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；0.1 M citrate 5.3, 15% (w/v) PEG 10K, 1.5% (v/v) dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.97 Å R-free 0.210
3S90 Human vinculin head domain Vh1 (residues 1-252) in complex with murine talin (VBS33; residues 1512-1546) Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–252（252 aa） Fragment：unp residues 1-252
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；0.1 M citrate 5.3, 15% (w/v) PEG 10K, 1.5% (v/v) dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.97 Å R-free 0.210
3TJ5 human vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding site of the surface cell antigen 4 (sca4-VBS-N; residues 412-434) from Rickettsia rickettsii Deposited 2011-08-23 Different construct 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 1–255（255 aa） Fragment：unp residues 1-255
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；0.1 M MES monohydrate pH 6.5, 14% PEG 20,000, 20 mM Tris-HCl pH 8, 150 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.218
3TJ6 human vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding site of the surface cell antigen 4 (sca4-VBS-C; residues 812-835) from Rickettsia rickettsii Deposited 2011-08-23 Different construct 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 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2% (v/v) tacsimate (pH 5), 100 mM sodium citrate tribasic dihydrate (pH 5.6), 16% (w/v) polyethylene glycol (3,350), 20 mM Tris-HCl (pH 9), 150 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.76 Å R-free 0.235
3TJ6 human vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding site of the surface cell antigen 4 (sca4-VBS-C; residues 812-835) from Rickettsia rickettsii Deposited 2011-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–257（257 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2% (v/v) tacsimate (pH 5), 100 mM sodium citrate tribasic dihydrate (pH 5.6), 16% (w/v) polyethylene glycol (3,350), 20 mM Tris-HCl (pH 9), 150 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.76 Å R-free 0.235
3VF0 Raver1 in complex with metavinculin L954 deletion mutant Deposited 2012-01-09 Different construct 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 856–1134（279 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 13 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.54 Å R-free 0.205
4DJ9 Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099) Deposited 2012-02-01 Different construct 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 1–258（258 aa） Fragment：unp residues 1-258
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；The human vinculin Vh1 domain (residues 1 - 258) was generated as described.9 Crystallization screens of Vh1 protein and VBS50 mixed in 1:5 molar ratio were performed at two temperatures. Co-crystals were obtained from Hampton crystal screen I with a reservoir of 0.1 M Hepes pH 7.5, 10% w/v polyethylene glycol 6,000, and 5% 2-Methyl-2,4-pentanediol. Crystals were transferred directly from the initial 96-well screening plate into Paratone-N oil and flash-frozen in liquid nitrogen. , VAPOR DIFFUSION
Resolution 2.25 Å R-free 0.247
4EHP Crystal Structure of human vinculin head domain (residues 1-252) in complex with alpha-catenin (residues 277-382) Deposited 2012-04-03 Different construct 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 1–252（252 aa） Fragment：unp residues 1-252
Not recorded ACT ACETATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；PEG 3350, sodium acetate, VAPOR DIFFUSION, temperature 295K
Resolution 2.66 Å R-free 0.229
4LN2 The second SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin Deposited 2013-07-11 Different construct 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 857–867（11 aa） Fragment：UNP residues 857-867
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；EVAPORATION
Resolution 1.00 Å R-free 0.152
4LNP The first SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin Deposited 2013-07-11 Different construct 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 870–879（10 aa） Fragment：proline rich peptide, UNP residues 870-879
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；293 K；pH 8.0, EVAPORATION, temperature 293K
Resolution 1.41 Å R-free 0.194
4PR9 Human Vinculin (residues 891-1066) in complex with PIP Deposited 2014-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 891–1066（176 aa） Fragment：C-terminal domain (UNP residues 891-1066 of isoform 1)
Chain B 891–1066（176 aa） Fragment：C-terminal domain (UNP residues 891-1066 of isoform 1)
Mutation：R1060A Mutation：R1060A PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；12% PEG3350, 2% tryptone, 0.05 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.20 Å R-free 0.250
4PR9 Human Vinculin (residues 891-1066) in complex with PIP Deposited 2014-03-05 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 C 891–1066（176 aa） Fragment：C-terminal domain (UNP residues 891-1066 of isoform 1)
Chain D 891–1066（176 aa） Fragment：C-terminal domain (UNP residues 891-1066 of isoform 1)
Mutation：R1060A Mutation：R1060A GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；12% PEG3350, 2% tryptone, 0.05 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.20 Å R-free 0.250
4PR9 Human Vinculin (residues 891-1066) in complex with PIP Deposited 2014-03-05 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 E 891–1066（176 aa） Fragment：C-terminal domain (UNP residues 891-1066 of isoform 1)
Chain F 891–1066（176 aa） Fragment：C-terminal domain (UNP residues 891-1066 of isoform 1)
Mutation：R1060A Mutation：R1060A PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；12% PEG3350, 2% tryptone, 0.05 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.20 Å R-free 0.250
5L0C Human metavinculin (residues 959-1134) in complex with PIP2 Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 959–1134（176 aa） Fragment：UNP Residues 959-1130
Chain C 959–1134（176 aa） Fragment：UNP Residues 959-1130
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20 mM citric acid, 80 mM Bis-Tris propane (pH 3.4), and 16% (w/v) PEG 3350
Resolution 3.10 Å R-free 0.261
5L0C Human metavinculin (residues 959-1134) in complex with PIP2 Deposited 2016-07-27 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 B 959–1134（176 aa） Fragment：UNP Residues 959-1130
Chain D 959–1134（176 aa） Fragment：UNP Residues 959-1130
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 3 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20 mM citric acid, 80 mM Bis-Tris propane (pH 3.4), and 16% (w/v) PEG 3350
Resolution 3.10 Å R-free 0.261
5L0D Human Metavinculin(residues 959-1130) in complex with PIP2 Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 959–1130（172 aa） Fragment：UNP Residues 959-1130
Chain B 959–1130（172 aa） Fragment：UNP Residues 959-1130
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.4；294 K；20 mM citric acid, 80-100 mM Bis-Tris propane (pH 3.4), and 12-16% (w/v) PEG 3350
Resolution 2.75 Å R-free 0.259
5L0D Human Metavinculin(residues 959-1130) in complex with PIP2 Deposited 2016-07-27 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 C 959–1130（172 aa） Fragment：UNP Residues 959-1130
Chain D 959–1130（172 aa） Fragment：UNP Residues 959-1130
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.4；294 K；20 mM citric acid, 80-100 mM Bis-Tris propane (pH 3.4), and 12-16% (w/v) PEG 3350
Resolution 2.75 Å R-free 0.259
5L0F Human metavinculin quadruple mutant (residues 959-1134) Deposited 2016-07-27 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 959–1134（176 aa） Fragment：UNP Residues 959-1134
Mutation：R975Q, K979Q, R1107Q, R1128Q GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；294 K；20 mM citric acid, 80 mM Bis-Tris propane (pH 8.8), and 14 to 16% (w/v) PEG 3350
Resolution 2.76 Å R-free 0.247
5L0F Human metavinculin quadruple mutant (residues 959-1134) Deposited 2016-07-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 959–1134（176 aa） Fragment：UNP Residues 959-1134
Mutation：R975Q, K979Q, R1107Q, R1128Q GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；294 K；20 mM citric acid, 80 mM Bis-Tris propane (pH 8.8), and 14 to 16% (w/v) PEG 3350
Resolution 2.76 Å R-free 0.247
5L0G Human metavinculin MVt Q971R, R975D, T978R mutant (residues 959-1134) in complex with PIP2 Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 959–1134（176 aa） Fragment：UNP Residues 959-1134
Chain B 959–1134（176 aa） Fragment：UNP Residues 959-1134
Mutation：Q971R, R975D, T978R Mutation：Q971R, R975D, T978R PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；12% PEG 3350, 2% tryptone, and 0.05 M HEPES
Resolution 3.40 Å R-free 0.221
5L0G Human metavinculin MVt Q971R, R975D, T978R mutant (residues 959-1134) in complex with PIP2 Deposited 2016-07-27 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 C 959–1134（176 aa） Fragment：UNP Residues 959-1134
Chain D 959–1134（176 aa） Fragment：UNP Residues 959-1134
Mutation：Q971R, R975D, T978R Mutation：Q971R, R975D, T978R PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；12% PEG 3350, 2% tryptone, and 0.05 M HEPES
Resolution 3.40 Å R-free 0.221
5L0H Human metavinculin MVt cardiomyopathy-associated mutant R975W (residues 959-1134) in complex with PIP2 Deposited 2016-07-27 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 959–1134（176 aa） Fragment：UNP Residues 959-1134
Mutation：R975W PEG DI(HYDROXYETHYL)ETHER × 1 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.2 M LiSO4, 0.1 M HEPES (pH 7.5), and 22% PEG 3350
Resolution 2.90 Å R-free 0.278
5L0I Human metavinculin MVt R975W cardiomyopathy-associated mutant (residues 959-1134) Deposited 2016-07-27 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 959–1134（176 aa） Fragment：UNP Residues 959-1134
Mutation：R975W GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1 M Na-citrate tribasic dihydrate, 2% Tacsimate (pH 5), and 16% PEG 3350
Resolution 2.45 Å R-free 0.238
5L0J Human vinculin R903Q, D907R, R910T mutant(residues 891-1066) Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 891–1066（176 aa）
Chain B 891–1066（176 aa）
Mutation：R903Q, D907R, R910T Mutation：R903Q, D907R, R910T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M HEPES sodium (pH 7.5), and 1.5 M Lithium sulfate monohydrate
Resolution 4.00 Å R-free 0.298
6UPW Metavinculin ABD-F-actin complex Deposited 2019-10-18 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 × 7 PDB declaration: heptameric
Chain L 1–1134（1134 aa）
Chain M 1–1134（1134 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7KTT Cryogenic electron microscopy model of full-length human metavinculin Deposited 2020-11-24 Different construct 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 1–1134（1134 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris, pH 8.0, 150 mM NaCl, 0.2 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.17 Å
7KTU Cryogenic electron microscopy model of full-length human metavinculin H1'-parallel conformation 1 Deposited 2020-11-24 Different construct 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 1–1134（1134 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris, pH 8.0, 150 mM NaCl, 0.2 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.15 Å
7KTV Cryogenic electron microscopy model of full-length human metavinculin H1' kinked conformation Deposited 2020-11-24 Different construct 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 1–1134（1134 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris, pH 8.0, 150 mM NaCl, 0.2 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7KTW Cryogenic electron microscopy model of full-length human metavinculin H1'-parallel conformation 2 Deposited 2020-11-24 Different construct 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 1–1134（1134 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris, pH 8.0, 150 mM NaCl, 0.2 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
9QWO Vinculin tail bound to paxillin LD2 Deposited 2025-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 891–1066（176 aa）
Chain B 891–1066（176 aa）
Chain C 891–1066（176 aa）
Chain D 891–1066（176 aa）
Not recorded SO4 SULFATE ION × 8 ACT ACETATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；1.26 M (NH4)2SO4, 0.2 M NaCl, 0.1 M Na Acetate pH4.5
Resolution 2.54 Å R-free 0.259

32 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VINC_HUMAN
Isoform P18206-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1066； UniProt 1–1066

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6fuy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6fuy
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6fuy
Deposition date deposition_date2018-02-28
Structure title titleCrystal structure of human full-length vinculin-T12-A974K (residues 1-1066)
Keywords keywordsMechanosensitive Self-inhibition Adapter, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier33.15 Å
Radius of gyration Rg (electron density) rg_electron32.58 Å
Forward intensity I(0) i0184818000.00
Molecular weight molecular_weight105170.0 kDa
Excluded volume excluded_volume130820 ų
Envelope volume envelope_volume176420 ų
Hydration-shell volume shell_volume45237 ų
Envelope diameter envelope_diameter118.0 Å
Shell Rg shell_rg39.21 Å
Envelope Rg envelope_rg32.17 Å
Shape Rg shape_rg32.58 Å
Total Rg total_rg33.10 Å
Total atoms total_atoms7351
Residues n_residues961
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax111.1 Å
Rg (real space) rg_real33.06 Å
Rg uncertainty (real space) rg_real_error0.78 Å
I(0) (real space) i0_real1.8480e+08
I(0) uncertainty (real space) i0_real_error2.3550e+06
Rg (reciprocal space) rg_reciprocal33.10 Å
I(0) (reciprocal space) i0_reciprocal184800000.0000
Solution quality estimate total_estimate0.8792
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.3 Å
Skewness Skewness skewness0.314
Kurtosis Kurtosis kurtosis-0.195
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19380000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.967
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6fuyA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily230 — Alpha-catenin/vinculin-like
Domain ID domain_id6fuyA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily230 — Alpha-catenin/vinculin-like
▶

8. Citations (1)

▶

9. Files and Curves (10)