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Yorodumi- PDB-1mhc: MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mhc | ||||||
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Title | MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION | ||||||
Components |
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Keywords | HISTOCOMPATIBILITY ANTIGEN/PEPTIDE / HISTOCOMPATIBILITY ANTIGEN-PEPTIDE complex | ||||||
Function / homology | Function and homology information Complex I biogenesis / alpha-beta T cell activation involved in immune response / Respiratory electron transport / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / cis-Golgi network membrane / response to xenobiotic stimulus => GO:0009410 / positive regulation of natural killer cell mediated cytotoxicity / response to hydroperoxide / Endosomal/Vacuolar pathway ...Complex I biogenesis / alpha-beta T cell activation involved in immune response / Respiratory electron transport / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / cis-Golgi network membrane / response to xenobiotic stimulus => GO:0009410 / positive regulation of natural killer cell mediated cytotoxicity / response to hydroperoxide / 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 / CD8 receptor binding / NADH:ubiquinone reductase (H+-translocating) / regulation of membrane depolarization / mitochondrial respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / cellular defense response / aerobic respiration / nitric oxide biosynthetic process / 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 / mitochondrial 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 / 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 / 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 nitric oxide biosynthetic process / positive regulation of immune response / positive regulation of type II interferon production / 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 / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / membrane => GO:0016020 / early endosome / 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 / neuronal cell body / dendrite / 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) Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Wang, C.-R. / Fischer Lindahl, K. / Deisenhofer, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3 Authors: Wang, C.R. / Castano, A.R. / Peterson, P.A. / Slaughter, C. / Lindahl, K.F. / Deisenhofer, J. #1: Journal: Cell(Cambridge,Mass.) / Year: 1991 Title: H-2M3 Encodes the Mhc Class I Molecule Presenting the Maternally Transmitted Antigen of the Mouse Authors: Wang, C.-R. / Loveland, B.E. / Fischer Lindahl, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mhc.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mhc.ent.gz | 138.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/1mhc ftp://data.pdbj.org/pub/pdb/validation_reports/mh/1mhc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 210 / 2: CIS PROLINE - PRO B 32 / 3: CIS PROLINE - PRO D 210 / 4: CIS PROLINE - PRO E 32 | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 D 2 .. D 182 A 2 .. A 182 0.288 M2 D 183 .. D 275 A 183 .. A 275 0.292 M3 E 1 .. E 99 B 1 .. B 99 0.312 |
-Components
#1: Protein | Mass: 32650.650 Da / Num. of mol.: 2 / Mutation: INS(275(A)-282(A)), INS(275(D)-282(D)) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3 B2M / Gene (production host): H2-M3 B2M / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q31093 #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 / Mutation: INS(275(A)-282(A)), INS(275(D)-282(D)) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3 B2M / Gene (production host): H2-M3 B2M / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887 #3: Protein/peptide | Mass: 1155.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P03889 #4: Sugar | ChemComp-NAG / | #5: 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: 2.34 Å3/Da / Density % sol: 47.52 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 26 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 33706 / % possible obs: 70 % / Rmerge(I) obs: 0.079 |
Reflection | *PLUS Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / % possible obs: 43 % |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |