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Yorodumi- PDB-2gww: Human vinculin (head domain, Vh1, residues 1-258) in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gww | ||||||
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Title | Human vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site (residues 602-633) | ||||||
Components |
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Keywords | CELL ADHESION / STRUCTURAL PROTEIN / protein complex | ||||||
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 / 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 / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / 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 / 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 / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.72 Å | ||||||
Authors | Izard, T. | ||||||
Citation | Journal: J.Cell Biol. / Year: 2006 Title: Shigella applies molecular mimicry to subvert vinculin and invade host cells. Authors: Izard, T. / Tran Van Nhieu, 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 | 2gww.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gww.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gww_validation.pdf.gz | 373.4 KB | Display | wwPDB validaton report |
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Full document | 2gww_full_validation.pdf.gz | 388.9 KB | Display | |
Data in XML | 2gww_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2gww_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/2gww ftp://data.pdbj.org/pub/pdb/validation_reports/gw/2gww | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30026.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P18206 |
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#2: Protein/peptide | Mass: 3310.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 32307018, UniProt: P18010*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.33 % |
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-Data collection
Diffraction |
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Diffraction source |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2.72→99 Å / Num. obs: 7633 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 73.693 Å2 |
-Processing
Software | Name: BUSTER-TNT / Version: 1.3.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.72→99 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: SOME OF THE WATER MOLECULES ARE PLACED IN DISORDERED DENSITY.
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Displacement parameters | Biso mean: 79.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4285 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.88 Å / Total num. of bins used: 9
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