+Open data
-Basic information
Entry | Database: PDB / ID: 2q86 | |||||||||
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Title | Structure of the mouse invariant NKT cell receptor Valpha14 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / iNKT cells / TCR / glycolipid recognition / innate immunity | |||||||||
Function / homology | Function and homology information Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / response to bacterium / adaptive immune response Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Zajonc, D.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal Structures of Mouse CD1d-iGb3 Complex and its Cognate Valpha14 T Cell Receptor Suggest a Model for Dual Recognition of Foreign and Self Glycolipids. Authors: Zajonc, D.M. / Savage, P.B. / Bendelac, A. / Wilson, I.A. / Teyton, L. | |||||||||
History |
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Remark 999 | SEQUENCE There is no UNP sequence reference available at the time of processing. There are ...SEQUENCE There is no UNP sequence reference available at the time of processing. There are following mutations present in the structure: chain A,C - F36Y, S46L, I89F, A102S, D115Y, T158C, 100-103 deleted, chain B,D - S167C. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q86.cif.gz | 359.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q86.ent.gz | 290.2 KB | Display | PDB format |
PDBx/mmJSON format | 2q86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/2q86 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/2q86 | HTTPS FTP |
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-Related structure data
Related structure data | 2q7yC 1tcrS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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Details | biological unit is a heterodimer consiting of Valpha14 chain and Vbeta8.2 chain |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 25399.354 Da / Num. of mol.: 2 / Fragment: extracellular domain Mutation: F36Y, S46L, I89F, A102S, D115Y, T158C, 100-103 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Valpha14 / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01849*PLUS #2: Protein | Mass: 28073.168 Da / Num. of mol.: 2 / Fragment: extracellular domain / Mutation: S167C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vbeta8.2 / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01851*PLUS |
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-Sugars , 3 types, 3 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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 |
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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 |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 546 molecules
#6: 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: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16% PEG 4000, 0.2 M magnesium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97976 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 11, 2006 / Details: flat mirror |
Radiation | Monochromator: single crystal Si(11) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97976 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 90127 / Num. obs: 90127 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TCR Resolution: 1.85→37.35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.498 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.122 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.322 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→37.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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