+Open data
-Basic information
Entry | Database: PDB / ID: 1mwa | ||||||||||||
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Title | 2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig domain / antigen recognition / complementarity determining region | ||||||||||||
Function / homology | Function and homology information positive regulation of cytochrome-c oxidase activity / TP53 Regulates Metabolic Genes / Respiratory electron transport / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex IV / alpha-beta T cell receptor complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...positive regulation of cytochrome-c oxidase activity / TP53 Regulates Metabolic Genes / Respiratory electron transport / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex IV / alpha-beta T cell receptor complex / 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 / regulation of membrane depolarization / antigen processing and presentation of exogenous peptide antigen via MHC class I / mitochondrial respiratory chain complex I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding / Neutrophil degranulation / 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 / mitochondrial 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 / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / mitochondrial inner membrane / learning or memory / defense response to Gram-positive bacterium / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Luz, J.G. / Huang, M.D. / Garcia, K.C. / Rudolph, M.G. / Teyton, L. / Wilson, I.A. | ||||||||||||
Citation | Journal: J.EXP.MED. / Year: 2002 Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation ...Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions. Authors: Luz, J.G. / Huang, M.D. / Garcia, K.C. / Rudolph, M.G. / Teyton, L. / Wilson, I.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mwa.cif.gz | 347.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mwa.ent.gz | 284.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/1mwa ftp://data.pdbj.org/pub/pdb/validation_reports/mw/1mwa | HTTPS FTP |
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-Related 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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-Components
-2C T CELL RECEPTOR ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 22298.889 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: GenBank: 224220, UniProt: P01738*PLUS #2: Protein | Mass: 26284.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: GenBank: 1791255, UniProt: P01851*PLUS |
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-Protein , 2 types, 4 molecules HILM
#3: Protein | Mass: 31719.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P01901 #4: Protein | Mass: 11704.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P01887 |
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-Protein/peptide , 1 types, 2 molecules PQ
#5: Protein/peptide | Mass: 1064.168 Da / Num. of mol.: 2 / Fragment: residues 54-61 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The peptide is naturally found in Mus musculus (Mouse). References: UniProt: Q62425 |
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-Sugars , 3 types, 6 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 679 molecules
#8: Chemical | #10: Chemical | ChemComp-ACY / | #11: 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: 3.25 Å3/Da / Density % sol: 62.17 % |
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Crystal grow | Temperature: 277.16 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.1M TRIS ACETATE, 12% PEG4000, 18% glycerol, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.16K |
-Data collection
Diffraction | Mean temperature: 104 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 |
Radiation | Monochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 95548 / % possible obs: 99.5 % / Rsym value: 0.052 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.453 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.39 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43932 / ESU R Free: 0.2997 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47.497 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→49.39 Å
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Refine LS restraints |
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