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Yorodumi- PDB-3e6h: MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e6h | ||||||
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Title | MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PI10, from the human immunodeficiency virus (BaL) envelope glycoprotein 120 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / COMPLEX (HISTOCOMPATIBILITY-ANTIGEN) / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Secreted / Envelope protein | ||||||
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 / Dectin-2 family / 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 / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / viral process / Neutrophil degranulation / host cell endosome membrane / 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 / 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 / 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 / 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 / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / viral protein processing / immune response / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Wang, R. / Natarajan, K. / Robinson, H. / Margulies, D.H. | ||||||
Citation | Journal: J.Immunol. / Year: 2009 Title: Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity Authors: Honda, M. / Wang, R. / Kong, W.P. / Kanekiyo, M. / Akahata, W. / Xu, L. / Matsuo, K. / Natarajan, K. / Robinson, H. / Asher, T.E. / Price, D.A. / Douek, D.C. / Margulies, D.H. / Nabel, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e6h.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e6h.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 3e6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e6h_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
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Full document | 3e6h_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 3e6h_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3e6h_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/3e6h ftp://data.pdbj.org/pub/pdb/validation_reports/e6/3e6h | HTTPS FTP |
-Related structure data
Related structure data | 3e6fC 1qo3S 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
#1: Protein | Mass: 32107.750 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01900 |
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#2: Protein | Mass: 11791.545 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m, RP23-34E24.5-001 / Plasmid: PET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q91XJ8, UniProt: P01887*PLUS |
#3: Protein/peptide | Mass: 1095.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A4L8F7, UniProt: P05877*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 11% PEG20000,0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→30 Å / Num. all: 30224 / Num. obs: 27990 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.101 / Χ2: 0.9 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.13→2.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 11.9 / Num. unique all: 2087 / Χ2: 0.479 / % possible all: 74.1 |
-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 1QO3 Resolution: 2.1→29.52 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 39.346 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.26 Å2 / Biso mean: 27.378 Å2 / Biso min: 7.39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.52 Å
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Refine LS restraints |
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Xplor file |
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