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- PDB-1u58: Crystal structure of the murine cytomegalovirus MHC-I homolog m144 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u58 | ||||||
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Title | Crystal structure of the murine cytomegalovirus MHC-I homolog m144 | ||||||
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![]() | IMMUNE SYSTEM / MCMV / MHC-I homolog / m144 / beta-2m | ||||||
Function / homology | ![]() 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 / cellular defense response / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, 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 / cellular defense response / Neutrophil degranulation / 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 / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Natarajan, K. / Hicks, A. / Robinson, H. / Guan, R. / Margulies, D.H. | ||||||
![]() | ![]() Title: Crystal structure of the murine cytomegalovirus MHC-I homolog m144. Authors: Natarajan, K. / Hicks, A. / Mans, J. / Robinson, H. / Guan, R. / Mariuzza, R.A. / Margulies, D.H. | ||||||
History |
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Remark 999 | SEQUENCE THE AMINO ACID SEQUENCE OF CHAIN A IS TRANSLATED FROM THE M144 OPEN READING FRAME AS FOUND ...SEQUENCE THE AMINO ACID SEQUENCE OF CHAIN A IS TRANSLATED FROM THE M144 OPEN READING FRAME AS FOUND IN MCMV GENOME, ACCESSION NUMBER NC_004065. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.7 KB | Display | ![]() |
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PDB format | ![]() | 62.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a6zS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28351.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Muromegalovirus / Gene: m144 / Plasmid: pET21-b / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 20K, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. all: 39025 / Num. obs: 36627 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.11 |
Reflection shell | Resolution: 1.87→1.94 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.8 / % possible all: 95.2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A6Z Resolution: 1.9→41.14 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012
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