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Yorodumi- PDB-3e3q: Structure of the 3alpham13 high-affinity mutant of the 2C TCR in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e3q | ||||||
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Title | Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR / MHC / high affinity / cross reactivity / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Receptor | ||||||
Function / homology | Function and homology information T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / adaptive immune response ...T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / adaptive immune response / immune response / external side of plasma membrane / signaling receptor binding / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å | ||||||
Authors | Colf, L.A. / Garcia, K.C. | ||||||
Citation | Journal: J.Immunol. / Year: 2008 Title: Distinct CDR3 conformations in TCRs determine the level of cross-reactivity for diverse antigens, but not the docking orientation. Authors: Jones, L.L. / Colf, L.A. / Stone, J.D. / Garcia, K.C. / Kranz, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e3q.cif.gz | 619.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e3q.ent.gz | 514.3 KB | Display | PDB format |
PDBx/mmJSON format | 3e3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e3q_validation.pdf.gz | 574.1 KB | Display | wwPDB validaton report |
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Full document | 3e3q_full_validation.pdf.gz | 601.6 KB | Display | |
Data in XML | 3e3q_validation.xml.gz | 98.9 KB | Display | |
Data in CIF | 3e3q_validation.cif.gz | 138.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3q ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3q | HTTPS FTP |
-Related structure data
Related structure data | 3e2hC 2oi9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 20541.621 Da / Num. of mol.: 8 / Fragment: UNP residues 25-199 Mutation: F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01897 #2: Protein/peptide | Mass: 1063.202 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse #3: Protein | Mass: 12071.595 Da / Num. of mol.: 8 / Mutation: L43P, W82R, G99D F100P A101P S102P A103L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01738, UniProt: Q5R1C2*PLUS #4: Protein | Mass: 12039.129 Da / Num. of mol.: 8 / Mutation: G17E, G42E, H47Y, I77T, L81S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 |
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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: 3.1 Å3/Da / Density % sol: 60.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, 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: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 30, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 93313 / % possible obs: 97.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Χ2: 1.117 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2 / Num. unique all: 9386 / Χ2: 1.005 / % possible all: 97.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2OI9 Resolution: 2.95→41.52 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 23.072 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.58 Å2 / Biso mean: 47.947 Å2 / Biso min: 18.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→41.52 Å
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Refine LS restraints |
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Xplor file |
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