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Yorodumi- PDB-1vad: MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN... -
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-Basic information
Entry | Database: PDB / ID: 1vad | ||||||
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Title | MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND YEAST ALPHA-GLUCOSIDASE | ||||||
Components |
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Keywords | COMPLEX (MHC I/PEPTIDE) / HISTOCOMPATIBILITY ANTIGEN / CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX / MHC I / COMPLEX (MHC I-PEPTIDE) COMPLEX | ||||||
Function / homology | Function and homology information Amino acid transport across the plasma membrane / glucan 1,4-alpha-maltotriohydrolase activity / disaccharide catabolic process / sucrose alpha-glucosidase activity / sucrose catabolic process / oligo-1,6-glucosidase activity / maltose catabolic process / maltose alpha-glucosidase activity / alpha-glucosidase / oligosaccharide catabolic process ...Amino acid transport across the plasma membrane / glucan 1,4-alpha-maltotriohydrolase activity / disaccharide catabolic process / sucrose alpha-glucosidase activity / sucrose catabolic process / oligo-1,6-glucosidase activity / maltose catabolic process / maltose alpha-glucosidase activity / alpha-glucosidase / oligosaccharide catabolic process / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / negative regulation of natural killer cell activation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / positive regulation of natural killer cell activation / alpha-amylase activity / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / negative regulation of T cell proliferation / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / positive regulation of type II interferon production / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Fremont, D.H. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Authors: Fremont, D.H. / Stura, E.A. / Matsumura, M. / Peterson, P.A. / Wilson, I.A. #1: Journal: Science / Year: 1992 Title: Crystal Structures of Two Viral Peptides in Complex with Murine Mhc Class I H-2Kb Authors: Fremont, D.H. / Matsumura, M. / Stura, E.A. / Peterson, P.A. / Wilson, I.A. #2: Journal: Science / Year: 1992 Title: Emerging Principles for the Recognition of Peptide Antigens by Mhc Class I Molecules Authors: Matsumura, M. / Fremont, D.H. / Peterson, P.A. / 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 | 1vad.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vad.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 1vad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vad ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vad | 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
#1: Protein | Mass: 31648.322 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/B / Gene: BETA-2-MICROGLOBULIN / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901 |
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/B / Gene: BETA-2-MICROGLOBULIN / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 1089.208 Da / Num. of mol.: 1 / Fragment: RESIDUES 438 - 446 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38158, alpha-glucosidase |
#4: Water | ChemComp-HOH / |
Sequence details | SOURCE MOLECULE_NAME: MALTASE, YEAST ALPHA-GLUCOSIDASE (RESIDUES 438 - 446). SOURCE OF PEPTIDE ...SOURCE MOLECULE_NAME: MALTASE, YEAST ALPHA-GLUCOSIDAS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % |
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 18677 / % possible obs: 91.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.068 |
-Processing
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Refinement | Resolution: 2.5→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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