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- PDB-3at0: Structural and biochemical characterization of ClfB:ligand intera... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3at0 | ||||||
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Title | Structural and biochemical characterization of ClfB:ligand interactions | ||||||
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![]() | CELL ADHESION/BLOOD CLOTTING / IgG like / Adhesin / Fibrinogen / cytokeratin / CELL ADHESION-BLOOD CLOTTING complex | ||||||
Function / homology | ![]() blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / cell adhesion / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ganesh, V.K. | ||||||
![]() | ![]() Title: Structural and biochemical characterization of ClfB:ligand interactions Authors: Ganesh, V.K. / Barbu, E.M. / Deivanayagam, C.C.S. / Le, B. / Anderson, A. / Matsuka, Y. / Lin, S.L. / Foster, T.J. / Narayana, S.V.L. / Hook, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.4 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.3 KB | Display | ![]() |
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Full document | ![]() | 441.7 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 37487.934 Da / Num. of mol.: 1 / Fragment: N2 N3 domain (UNP RESIDUES 212-541) / Mutation: D444E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1483.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 0.9M sodium citrate, 90mM imidazole pH 8.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 21349 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.63 Å2 / Biso mean: 25.8039 Å2 / Biso min: 10.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→28.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.501→2.565 Å / Total num. of bins used: 20
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