4dj9

Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099)

Method: X-RAY DIFFRACTION D_max: 93.8 Å Quality: GOOD

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

Vinculin

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–258	Fragment：unp residues 1-258	Talin-1 × 1 （Q9Y490）	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

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 4DJ9	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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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
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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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
6FUY Crystal structure of human full-length vinculin-T12-A974K (residues 1-1066) Deposited 2018-02-28	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	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
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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1134（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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1134（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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1134（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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1134（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	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 1–258

Talin-1

Homo sapiens

UniProt Q9Y490

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 2075–2103	Fragment：unp residues 2075-2103	Vinculin × 1 （P18206）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4DJ9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 607–631（25 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 experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 607–631（25 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 experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 607–631（25 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
2MWN Talin-F3 / RIAM N-terminal Peptide complex Deposited 2014-11-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 308–400（93 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.5 mM [U-15N] Talin-F3, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 1 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM RIAM-N peptide, 0.5 mM [U-15N; U-2H] Talin-F3, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 1 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6R9T Cryo-EM structure of autoinhibited human talin-1 Deposited 2019-04-04	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 1–2541（2541 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blotted 4 seconds before plunging, blot force 4	Resolution 6.20 Å

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TLN1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–29； UniProt 2075–2103

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4dj9
Deposition date deposition_date	2012-02-01
Structure title title	Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099)
Keywords keywords	cytoskeleton, focal adhesion, protein-protein interaction, four-helix bundle, cell adhesion, F-actin, cytosol; 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	25.70 Å
Radius of gyration Rg (electron density) rg_electron	25.76 Å
Forward intensity I(0) i0	13791800.00
Molecular weight molecular_weight	28749.0 kDa
Excluded volume excluded_volume	36399 Å³
Envelope volume envelope_volume	45463 Å³
Hydration-shell volume shell_volume	17102 Å³
Envelope diameter envelope_diameter	96.9 Å
Shell Rg shell_rg	28.75 Å
Envelope Rg envelope_rg	26.16 Å
Shape Rg shape_rg	25.79 Å
Total Rg total_rg	26.08 Å
Total atoms total_atoms	2012
Residues n_residues	264
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	93.8 Å
Rg (real space) rg_real	26.14 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	1.3790e+07
I(0) uncertainty (real space) i0_real_error	2.1510e+05
Rg (reciprocal space) rg_reciprocal	26.00 Å
I(0) (reciprocal space) i0_reciprocal	13790000.0000
Solution quality estimate total_estimate	0.7547
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.690
Kurtosis Kurtosis kurtosis	-0.076
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3648000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.512; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.321; Smooth: 0.949

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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	28937.4 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	2103

MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 2 Entity 2 polymer

Description description	Talin-1
Molecular weight formula_weight	2870.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ETQVVLINAVKDVAKALGDLISATKAAAG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4dj9a1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.9 — alpha-catenin/vinculin-like
Family Family family	a.24.9.1 — alpha-catenin/vinculin

Domain ID domain_id	d4dj9a2
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.9 — alpha-catenin/vinculin-like
Family Family family	a.24.9.1 — alpha-catenin/vinculin

CATH v4.4 (2 domains)

Domain ID domain_id	4dj9A01
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	4dj9A02
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	33.540 Å
Unit-cell length b length_b	68.160 Å
Unit-cell length c length_c	137.600 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	68.800 Å
R factor r_factor	0.2095
R_work r_work	0.2076
R_free r_free	0.2472

fit	/app/data/saxs_computation/dj/4dj9/4dj9.fit
pddf	/app/data/pr_computation/dj/4dj9/4dj9.pr.out
profile	/app/data/saxs_computation/dj/4dj9/4dj9.dat

Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099)

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-1

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)