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Yorodumi- PDB-6m2k: Uncommon structural features of rabbit MHC class I (RLA-A1) compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m2k | ||||||
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Title | Uncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit haemorrhagic disease virus (RHDV) derived peptide, VP60-10 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC I complex / VP60-10 | ||||||
Function / homology | Function and homology information calicivirin / antigen processing and presentation of peptide antigen via MHC class I / ribonucleoside triphosphate phosphatase activity / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding ...calicivirin / antigen processing and presentation of peptide antigen via MHC class I / ribonucleoside triphosphate phosphatase activity / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / 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 / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / viral capsid / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / RNA helicase activity / learning or memory / immune response / RNA-directed RNA polymerase / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / viral RNA genome replication / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / Golgi membrane / RNA-dependent RNA polymerase activity / focal adhesion / DNA-templated transcription / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / proteolysis / extracellular space / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) Rabbit hemorrhagic disease virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Zhang, Q.X. / Liu, K.F. / Yue, C. / Zhang, D. / Lu, D. / Xiao, W.L. / Liu, P.P. / Zhao, Y.Z. / Gao, G.L. / Ding, C.M. ...Zhang, Q.X. / Liu, K.F. / Yue, C. / Zhang, D. / Lu, D. / Xiao, W.L. / Liu, P.P. / Zhao, Y.Z. / Gao, G.L. / Ding, C.M. / Lyu, J.X. / Liu, W.J. | ||||||
Citation | Journal: J.Virol. / Year: 2020 Title: Strict Assembly Restriction of Peptides from Rabbit Hemorrhagic Disease Virus Presented by Rabbit Major Histocompatibility Complex Class I Molecule RLA-A1. Authors: Zhang, Q. / Liu, K. / Yue, C. / Zhang, D. / Lu, D. / Xiao, W. / Liu, P. / Zhao, Y. / Gao, G. / Ding, C. / Lyu, J. / Liu, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m2k.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2k.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 6m2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2k ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2k | HTTPS FTP |
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-Related structure data
Related structure data | 6m24C 6m2jC 5degS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1034.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rabbit hemorrhagic disease virus / References: UniProt: P27410*PLUS |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein | Mass: 31676.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli) / References: UniProt: P06140 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS PH 6.5, 20% w/v PEG 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03923 Å |
Detector | Type: SDMS / Detector: CMOS / Date: Oct 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03923 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 18060 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 37.86 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 2.78 |
Reflection shell | Resolution: 2.59→2.69 Å / Rmerge(I) obs: 0.758 / Num. unique obs: 18060 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DEG Resolution: 2.59→29.97 Å / SU ML: 0.406 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.1048
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→29.97 Å
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Refine LS restraints |
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LS refinement shell |
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