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Yorodumi- PDB-3mj7: Crystal structure of the complex of JAML and Coxsackie and Adenov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mj7 | |||||||||
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Title | Crystal structure of the complex of JAML and Coxsackie and Adenovirus receptor, CAR | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN TANDEM DOMAIN / IMMUNE RECEPTOR COMPLEX / CELL ADHESION / CELL JUNCTION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / TRANSMEMBRANE / COSTIMULATION / PHOSPHOPROTEIN / RECEPTOR / SECRETED / TIGHT JUNCTION | |||||||||
Function / homology | Function and homology information monocyte extravasation / 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 / neutrophil extravasation ...monocyte extravasation / 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 / neutrophil extravasation / 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 / intercalated disc / bicellular tight junction / mitochondrion organization / cell adhesion molecule binding / 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 homodimerization activity / protein-containing complex / extracellular space / nucleoplasm / nucleus / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Verdino, P. / Wilson, I.A. | |||||||||
Citation | Journal: Science / Year: 2010 Title: The molecular interaction of CAR and JAML recruits the central cell signal transducer PI3K. Authors: Verdino, P. / Witherden, D.A. / Havran, W.L. / Wilson, I.A. #1: Journal: Science / Year: 2010 Title: The junctional adhesion molecule JAML is a costimulatory receptor for epithelial gammadelta T cell activation. Authors: Witherden, D.A. / Verdino, P. / Rieder, S.E. / Garijo, O. / Mills, R.E. / Teyton, L. / Fischer, W.H. / Wilson, I.A. / Havran, W.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mj7.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mj7.ent.gz | 152.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/3mj7 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/3mj7 | 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: 30647.387 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 21-280) / Mutation: K124R, R211Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Amica1, Gm638, Jaml / Plasmid: PMT/BIP/V5-HIS A / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q80UL9 |
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#2: Protein | Mass: 25046.229 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 18-236) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Car, Cxadr / Plasmid: PBAC6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97792 |
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.25 M LI-SULFATE, 0.1 M MES, 24% PEG 3350, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2007 Details: SI(111) DOUBLE CRYSTAL MONOCHROMETER. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY |
Radiation | Monochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 14679 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.529 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.92 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 40.735 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R: 2.932 / ESU R Free: 0.391 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.212 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 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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