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Yorodumi- PDB-5m00: Crystal structure of murine P14 TCR complex with H-2Db and Y4A, m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m00 | ||||||
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Title | Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide from LCMV | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class I / TCR / H-2Db / gp33 / LCMV | ||||||
Function / homology | Function and homology information Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Achour, A. / Sandalova, T. / Sun, R. / Han, X. | ||||||
Citation | Journal: To Be Published Title: Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant Authors: Allerbring, E. / Duru, A. / Sun, R. / Han, X. / Uchtenhagen, H. / Madhurantakam, C. / Popov, A. / Markova, N. / Talyzina, A. / Nygren, P.A. / Sandalova, T. / Achour, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m00.cif.gz | 346.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m00.ent.gz | 280.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m00_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 5m00_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 5m00_validation.xml.gz | 33 KB | Display | |
Data in CIF | 5m00_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/5m00 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/5m00 | HTTPS FTP |
-Related structure data
Related structure data | 5m01C 5m02C 5tjeC 1s7uS 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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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABH
#1: Protein | Mass: 32087.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899 |
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#2: Protein | Mass: 13794.978 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 |
#4: Protein | Mass: 26647.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P04213, UniProt: Q7TND8 |
-Antibody / Protein/peptide / Non-polymers , 3 types, 383 molecules GP
#3: Antibody | Mass: 23072.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trav14-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2JF94, UniProt: Q6PIR9 |
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#5: Protein/peptide | Mass: 953.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#6: Water | ChemComp-HOH / |
-Details
Has protein modification | Y |
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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: 2.75 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 19% PEG 6000, 0.1M Tris HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→128.9 Å / Num. obs: 77777 / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.548 / Num. unique all: 4274 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1s7u Resolution: 1.95→128.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.914 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.145 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.426 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→128.87 Å
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