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Yorodumi- PDB-1zhb: Crystal Structure Of The Murine Class I Major Histocompatibility ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zhb | ||||||
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Title | Crystal Structure Of The Murine Class I Major Histocompatibility Complex Of H-2Db, B2-Microglobulin, and a 9-Residue Peptide Derived from rat dopamine beta-monooxigenase | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / TCR-crossreactivity / self-ligand / autoimmunity | ||||||
Function / homology | Function and homology information octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / Catecholamine biosynthesis / homoiothermy / : / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway ...octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / Catecholamine biosynthesis / homoiothermy / : / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / norepinephrine biosynthetic process / varicosity / chromaffin granule membrane / response to ozone / response to xenobiotic stimulus => GO:0009410 / response to isolation stress / behavioral response to ethanol / catecholamine metabolic process / dopamine catabolic process / maternal behavior / fear response / L-ascorbic acid binding / response to iron ion / response to copper ion / 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 / transport vesicle membrane / response to pain / leukocyte migration / regulation of membrane depolarization / social behavior / associative learning / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / response to immobilization stress / blood vessel remodeling / cellular response to manganese ion / cellular defense response / beta-2-microglobulin binding / positive regulation of vasoconstriction / response to amphetamine / 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 / secretory granule membrane / locomotory behavior / 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 / visual learning / bone development / 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 / response to organic cyclic compound / terminal bouton / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / memory / positive regulation of T cell cytokine production / response to peptide hormone / 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 / sensory perception of taste / 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 / apical part of cell / response to estradiol / negative regulation of neuron projection development / MHC class II protein complex binding / glucose homeostasis / late endosome membrane / positive regulation of cold-induced thermogenesis / T cell differentiation in thymus / regulation of cell population proliferation / iron ion transport / protein refolding / cytoplasmic vesicle Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sandalova, T. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Schneider, G. / Karre, K. / Achour, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: A structural basis for CD8+ T cell-dependent recognition of non-homologous peptide ligands: implications for molecular mimicry in autoreactivity Authors: Sandalova, T. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Schneider, G. / Karre, K. / Achour, A. #1: Journal: Immunity / Year: 2002 Title: A structural basis for LCMV immune evasion: subversion of H-2D(b) and H-2K(b) presentation of gp33 revealed by comparative crystal structure.Analyses Authors: Achour, A. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Grufman, P. / Sandberg, J.K. / Levitsky, V. / Karre, K. / Sandalova, T. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zhb.cif.gz | 312.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zhb.ent.gz | 256.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/1zhb ftp://data.pdbj.org/pub/pdb/validation_reports/zh/1zhb | HTTPS FTP |
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-Related structure data
Related structure data | 1n5aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: EXTRAcellular part Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D / Production host: Escherichia coli (E. coli) / References: UniProt: P01899 #2: Protein | Mass: 11704.359 Da / Num. of mol.: 4 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 #3: Protein/peptide | Mass: 1053.231 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q05754, dopamine beta-monooxygenase #4: 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: 3.3 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: ammonium sulphate, Tris HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0292 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0292 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. all: 203819 / Num. obs: 58548 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 66.2 Å2 / Rsym value: 0.081 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 2200 / Rsym value: 0.502 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N5A Resolution: 2.7→24.92 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.907 / SU B: 23.57 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.378 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.366 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→24.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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