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Yorodumi- PDB-3mj6: Crystal structure of the gammadelta T cell costimulatory receptor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mj6 | |||||||||
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Title | Crystal structure of the gammadelta T cell costimulatory receptor Junctional Adhesion Molecule-Like Protein, JAML | |||||||||
Components | Junctional adhesion molecule-like | |||||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN TANDEM DOMAIN / CELL ADHESION / CELL JUNCTION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / COSTIMULATION / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information monocyte extravasation / Cell surface interactions at the vascular wall / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis ...monocyte extravasation / Cell surface interactions at the vascular wall / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / integrin binding / protein homodimerization activity / nucleoplasm / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 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 | 3mj6.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mj6.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 3mj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/3mj6 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/3mj6 | 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
-Protein , 1 types, 1 molecules A
#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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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar |
-Non-polymers , 3 types, 138 molecules
#4: Chemical | ChemComp-NA / | ||
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#5: Chemical | ChemComp-FMT / #6: 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: 2.58 Å3/Da / Density % sol: 52.36 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: 3.25 M NA-FORMATE, 0.1 M IMIDAZOLE, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.07812, 0.99984 | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2005 / Details: KOHZU: DOUBLE CRYSTAL SI(111) | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.19→50 Å / Num. obs: 15924 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.1 | |||||||||
Reflection shell | Resolution: 2.19→2.24 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2 / Rsym value: 0.415 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: OBTAINED BY MAD PHASING OF A TA6BR12 SOAKED JAML CRYSTAL AND SUBSEQUENT MR INTO THE NATIVE HIGH RESOLUTION DATA Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.735 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS WAS ALSO USED FOR THE REFINEMENT.
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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: 37.609 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.25 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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