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- PDB-1syq: Human vinculin head domain VH1, residues 1-258, in complex with h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1syq | ||||||
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Title | Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin binding site 1, residues 607-636 | ||||||
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![]() | CELL ADHESION / cytoskeleton / vinculin / talin | ||||||
Function / homology | ![]() regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding / alpha-catenin binding / vinculin binding / XBP1(S) activates chaperone genes / fascia adherens / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cell-cell contact zone / integrin activation / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / cell-substrate junction assembly / axon extension / protein localization to cell surface / cell-cell junction assembly / lamellipodium assembly / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / maintenance of blood-brain barrier / p130Cas linkage to MAPK signaling for integrins / phosphatidylserine binding / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / Smooth Muscle Contraction / ruffle / Integrin signaling / negative regulation of cell migration / phosphatidylinositol binding / cell-matrix adhesion / cell projection / integrin-mediated signaling pathway / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / sarcolemma / beta-catenin binding / platelet aggregation / ruffle membrane / cell-cell adhesion / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / extracellular vesicle / actin filament binding / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / cell surface / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Izard, T. / Vonrhein, C. | ||||||
![]() | ![]() Title: Structural basis for amplifying vinculin activation by talin Authors: Izard, T. / Vonrhein, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.6 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.2 KB | Display | ![]() |
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Full document | ![]() | 381.8 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29766.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2421.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q9Y490 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.59 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97889 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→50 Å / Num. obs: 15061 / % possible obs: 97.6 % / Redundancy: 18 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.179 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.42→2.51 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3 / % possible all: 80.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.5471 Å2 / ksol: 0.322653 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.42→32.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.57 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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