+Open data
-Basic information
Entry | Database: PDB / ID: 3rwd | ||||||
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Title | rhesus macaque MHC class I molecule Mamu-B*17-IW11 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antigenic peptides / T lymphocytes / immune response | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen via MHC class I / virus-mediated perturbation of host defense response / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation ...antigen processing and presentation of peptide antigen via MHC class I / virus-mediated perturbation of host defense response / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 / T cell differentiation in thymus / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / receptor-mediated endocytosis of virus by host cell / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / GTP binding / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) Simian immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.602 Å | ||||||
Authors | Wu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Price, D.A. / Gao, G.F. | ||||||
Citation | Journal: J.Immunol. / Year: 2011 Title: Structural basis of diverse peptide accommodation by the rhesus macaque MHC class I molecule Mamu-B*17: insights into immune protection from simian immunodeficiency virus Authors: Wu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Gostick, E. / Price, D.A. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rwd.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rwd.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 3rwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/3rwd ftp://data.pdbj.org/pub/pdb/validation_reports/rw/3rwd | HTTPS FTP |
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-Related structure data
Related structure data | 3rwcC 3rweC 3rwfC 3rwgC 3rwhC 3rwiC 3rwjC 2bvoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32025.082 Da / Num. of mol.: 2 / Fragment: residues 24-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: MHCI-B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GJ77 #2: Protein | Mass: 11660.079 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V7J5 #3: Protein/peptide | Mass: 1468.742 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthtic peptide / Source: (synth.) Simian immunodeficiency virus / References: UniProt: Q5QGG3 #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: 2.78 Å3/Da / Density % sol: 55.77 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
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Detector | Date: Jun 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 28767 / Biso Wilson estimate: 26.49 Å2 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BVO Resolution: 2.602→27.276 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.782 / SU ML: 0.38 / σ(F): 1.98 / Phase error: 29.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.317 Å2 / ksol: 0.321 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.77 Å2 / Biso mean: 29.153 Å2 / Biso min: 7.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.602→27.276 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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