[English] 日本語
Yorodumi- PDB-1rjz: Mhc Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With bet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rjz | ||||||
---|---|---|---|---|---|---|---|
Title | Mhc Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and Herpies Simplex Virus Mutant Glycoprotein B Peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / MHC / class I / virus / TCR / herpes | ||||||
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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell Golgi membrane / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell Golgi membrane / inner ear development / 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 / host cell endosome membrane / peptide binding / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / amyloid fibril formation / learning or memory / defense response to bacterium / symbiont entry into host cell / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Miley, M.J. / Messaoudi, I. / Nikolich-Zugich, J. / Fremont, D.H. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2004 Title: Structural Basis for the Restoration of TCR Recognition of an MHC Allelic Variant by Peptide Secondary Anchor Substitution Authors: Miley, M.J. / Messaoudi, I. / Metzner, B.M. / Wu, Y. / Nikolich-Zugich, J. / Fremont, D.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rjz.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rjz.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rjz_validation.pdf.gz | 399.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rjz_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 1rjz_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1rjz_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/1rjz ftp://data.pdbj.org/pub/pdb/validation_reports/rj/1rjz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32179.900 Da / Num. of mol.: 2 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901 #2: Protein | Mass: 11835.555 Da / Num. of mol.: 2 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: 965.082 Da / Num. of mol.: 2 / Mutation: S2E / Source method: obtained synthetically Details: naturally occuring sequence in herpies simplex virus with S2E point mutation References: UniProt: P06436 #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, ca Acetate, sodium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2003 / Details: Yale Mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 29043 / Num. obs: 29043 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 8.76 |
Reflection shell | Resolution: 2.6→2.7 Å / Mean I/σ(I) obs: 1.77 / Rsym value: 0.421 / % possible all: 93.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.94 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 184621.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.8645 Å2 / ksol: 0.304248 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.94 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|