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Yorodumi- PDB-3jz7: Crystal structure of the extracellular domains of coxsackie & ade... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jz7 | ||||||
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Title | Crystal structure of the extracellular domains of coxsackie & adenovirus receptor from mouse (mCAR) | ||||||
Components | Coxsackievirus and adenovirus receptor homolog | ||||||
Keywords | CELL ADHESION / cell adhesion molecule / immunoglobuline superfamily / adenovirus / coxsackievirus / Alternative splicing / Cell junction / Cell membrane / Disulfide bond / Glycoprotein / Immunoglobulin domain / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Receptor / Secreted / Tight junction / Transmembrane | ||||||
Function / homology | Function and homology information AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / Cell surface interactions at the vascular wall / negative regulation of cardiac muscle cell proliferation / gamma-delta T cell activation / regulation of AV node cell action potential / positive regulation of epithelial cell proliferation involved in wound healing ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / Cell surface interactions at the vascular wall / negative regulation of cardiac muscle cell proliferation / gamma-delta T cell activation / regulation of AV node cell action potential / positive regulation of epithelial cell proliferation involved in wound healing / germ cell migration / apicolateral plasma membrane / cell-cell junction organization / transepithelial transport / connexin binding / cardiac muscle cell development / cardiac muscle cell proliferation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / intercalated disc / cell adhesion molecule binding / mitochondrion organization / neutrophil chemotaxis / acrosomal vesicle / filopodium / PDZ domain binding / adherens junction / neuromuscular junction / cell-cell adhesion / beta-catenin binding / cell-cell junction / integrin binding / cell junction / cell body / heart development / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / neuron projection / membrane raft / signaling receptor binding / protein-containing complex / extracellular space / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å | ||||||
Authors | Max, K.E.A. / Heinemann, U. | ||||||
Citation | Journal: J.Neurosci. / Year: 2010 Title: The coxsackievirus-adenovirus receptor reveals complex homophilic and heterophilic interactions on neural cells. Authors: Patzke, C. / Max, K.E. / Behlke, J. / Schreiber, J. / Schmidt, H. / Dorner, A.A. / Kroger, S. / Henning, M. / Otto, A. / Heinemann, U. / Rathjen, F.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jz7.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jz7.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/3jz7 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/3jz7 | HTTPS FTP |
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-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: 23730.842 Da / Num. of mol.: 1 / Fragment: D1 & D2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Car, Cxadr / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P97792 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.78 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: protein buffer: 20mM TRIS 50mM NaCl protein concentration: 8mg / ml; crystallization buffer 0.1M HEPES pH 7.5 21% PEG 4000 15% isopropanol; crystalliztion setup: mixture 400nl protein sample ...Details: protein buffer: 20mM TRIS 50mM NaCl protein concentration: 8mg / ml; crystallization buffer 0.1M HEPES pH 7.5 21% PEG 4000 15% isopropanol; crystalliztion setup: mixture 400nl protein sample : 400nl crystallization buffer reservoir filled with 80 ul crystallization buffer; cryo solution: 25% PEG 4000 20% isopropanol 10% glycerol 0.1M HEPES pH 7.5 freezing of crystals: crystallization setup was overlayed with cryosolution, floating crystals were removed with a cryoloop and flash-frozen in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 16, 2008 Details: Mirror 1: Silicon, active surface 50nm Rh-coated. Double crystal monochromator: Si-111 crystal. Mirror 2: Glas, active surface 50nm Rh-coated |
Radiation | Monochromator: Mirrors & silicon-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→50 Å / Num. obs: 15245 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 47.774 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.003 / Net I/σ(I): 13.63 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.37 / Num. unique all: 1481 / Χ2: 0.999 / % possible all: 98.2 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_FTF
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EAJ (complete) for domain D1 2V5R (residues 5-40, 44-62, 68-76, 81-90) for domain D2 Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.783 / SU B: 6.441 / SU ML: 0.163 / SU R Cruickshank DPI: 0.231 / SU Rfree: 0.208 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.05 Å2 / Biso mean: 38.075 Å2 / Biso min: 30.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.144 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.188→2.245 Å / Total num. of bins used: 20
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