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- PDB-1mhc: MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED ... -
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Open data
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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 | ||||||
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![]() | HISTOCOMPATIBILITY ANTIGEN/PEPTIDE / HISTOCOMPATIBILITY ANTIGEN-PEPTIDE complex | ||||||
Function / homology | ![]() 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 / response to xenobiotic stimulus => GO:0009410 / positive regulation of natural killer cell mediated cytotoxicity / response to hydroperoxide / Endosomal/Vacuolar pathway / DAP12 interactions ...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 / 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 / NADH:ubiquinone reductase (H+-translocating) / : / NADH dehydrogenase (ubiquinone) activity / cellular defense response / nitric oxide biosynthetic process / aerobic respiration / 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 / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / response to organic cyclic compound / 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 / positive regulation of cellular senescence / peptide antigen binding / 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 nitric oxide biosynthetic process / positive regulation of type II interferon production / 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 / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / neuronal cell body / dendrite / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Wang, C.-R. / Fischer Lindahl, K. / Deisenhofer, J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.4 KB | Display | ![]() |
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PDB format | ![]() | 138.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.1 KB | Display | ![]() |
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Full document | ![]() | 487.5 KB | Display | |
Data in XML | ![]() | 34.3 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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 |
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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.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1155.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Sugar | ChemComp-NAG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 % |
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Processing
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |