+Open data
-Basic information
Entry | Database: PDB / ID: 3rf3 | ||||||
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Title | Shigella IpaA-VBS3 in complex with human vinculin | ||||||
Components |
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Keywords | protein binding/toxin / alpha-helix bundle domain / cytoskeletal protein / protein-protein interactions / cell adhesion / cytoskeleton / bacterial toxins / pathogen-host interactions / IpaA / Talin / F-actin / phosphatidylinositol 4 5-bisphosphate / Cytosol / Focal adhesion / protein binding-toxin 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 / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Park, H. / Sharff, A. / Izard, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Novel vinculin binding site of the IpaA invasin of Shigella. Authors: Park, H. / Valencia-Gallardo, C. / Sharff, A. / Tran Van Nhieu, G. / Izard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rf3.cif.gz | 461.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rf3.ent.gz | 384.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rf3_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
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Full document | 3rf3_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 3rf3_validation.xml.gz | 29 KB | Display | |
Data in CIF | 3rf3_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/3rf3 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/3rf3 | HTTPS FTP |
-Related structure data
Related structure data | 2gwwS S: Starting model for refinement |
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Similar 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: 28937.398 Da / Num. of mol.: 2 / Fragment: unp residues 1-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCL, vinculin / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18206 #2: Protein/peptide | Mass: 3139.582 Da / Num. of mol.: 2 / Fragment: unp residues 488-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: CP0125, ipaA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18010 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.2 Details: 0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→137 Å / Num. all: 82558 / Num. obs: 82474 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 26.24 Å2 / Rsym value: 0.037 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.61→1.7 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 11885 / Rsym value: 0.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2gww Resolution: 1.61→53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9548 / SU R Cruickshank DPI: 0.102 / Isotropic thermal model: isotropic + TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.188 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.65 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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