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Yorodumi- PDB-1rkc: Human vinculin head (1-258) in complex with talin's vinculin bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rkc | ||||||
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Title | Human vinculin head (1-258) in complex with talin's vinculin binding site 3 (residues 1944-1969) | ||||||
Components |
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Keywords | cell adhesion / structural protein / cytoskeleton / actin-binding / x-ray crystallography | ||||||
Function / homology | Function and homology information 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 / dystroglycan binding / alpha-catenin 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 / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / apical junction assembly / adherens junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / ruffle / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / cell-cell adhesion / ruffle membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / sarcolemma / platelet aggregation / beta-catenin binding / actin filament binding / specific granule lumen / integrin binding / 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 / Signaling by ALK fusions and activated point mutants / 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 | Homo sapiens (human) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Izard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Vinculin activation by talin through helical bundle conversion Authors: Izard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rkc.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rkc.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rkc_validation.pdf.gz | 370.8 KB | Display | wwPDB validaton report |
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Full document | 1rkc_full_validation.pdf.gz | 402.5 KB | Display | |
Data in XML | 1rkc_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1rkc_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/1rkc ftp://data.pdbj.org/pub/pdb/validation_reports/rk/1rkc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29489.982 Da / Num. of mol.: 1 / Fragment: vinculin head (residues 1-258) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli (E. coli) / References: UniProt: P18206 |
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#2: Protein/peptide | Mass: 2905.392 Da / Num. of mol.: 1 / Fragment: binding site 3 (residues 1944-1969) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P54939 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 4 Details: 2% MPD; 100 mM citric acid (pH 4); 100 mM CdCl2, pH 4.0, temperature 293K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4 / Method: vapor diffusion | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,1.2545,0.9793 | |||||||||
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Detector | Detector: CCD | |||||||||
Radiation | Protocol: MIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→15 Å / Num. all: 9051 / Num. obs: 9051 / Observed criterion σ(I): 0 / Biso Wilson estimate: 99.3 Å2 | |||||||||
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 45 Å / Num. all: 9121 / % possible obs: 99.8 % / Redundancy: 19.6 % / Num. measured all: 178681 / Rmerge(I) obs: 0.1 | |||||||||
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å / % possible obs: 99.7 % / Redundancy: 5.4 % / Num. unique obs: 1290 / Num. measured obs: 6993 / Rmerge(I) obs: 0.497 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 90 Å2 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.9 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.78 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.248 / Total num. of bins used: 9 | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_bond_d / Dev ideal: 0.01 | ||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.7 Å |