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Yorodumi- PDB-2ibf: Human vinculin's head domain (Vh1, residues 1-258) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ibf | ||||||
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Title | Human vinculin's head domain (Vh1, residues 1-258) in complex with two vinculin binding sites of Shigella flexneri's IpaA (residues 565-587) | ||||||
Components |
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Keywords | CELL ADHESION / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of actin filament depolymerization / 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 ...positive regulation of actin filament depolymerization / 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 / vinculin binding / fascia adherens / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / sarcolemma / MAP2K and MAPK activation / platelet aggregation / beta-catenin binding / 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 / extracellular vesicle / Signaling by BRAF and RAF1 fusions / cell-cell junction / 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 / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Izard, T. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Vinculin binding in its closed conformation by a helix addition mechanism. Authors: Nhieu, G.T. / Izard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ibf.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ibf.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ibf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/2ibf ftp://data.pdbj.org/pub/pdb/validation_reports/ib/2ibf | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 30026.590 Da / Num. of mol.: 1 / Fragment: Head domain (Vh1): 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: 2752.103 Da / Num. of mol.: 2 / Fragment: Vinculin binding sites: Residues 565-587 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaA / Production host: Escherichia coli (E. coli) / References: UniProt: P18010 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.41 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.2→109.11 Å / Num. obs: 10911 / Biso Wilson estimate: 95.717 Å2 |
Reflection shell | Highest resolution: 3.2 Å |
-Processing
Software | Name: BUSTER-TNT / Version: 1.3.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→109.11 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 74.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.73 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→109.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.39 Å / Total num. of bins used: 9
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