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- PDB-6m2j: Uncommon structural features of rabbit MHC class I (RLA-A1) compl... -
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Basic information
Entry | Database: PDB / ID: 6m2j | ||||||
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Title | Uncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit haemorrhagic disease virus (RHDV) derived peptide, VP60-1 | ||||||
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![]() | IMMUNE SYSTEM / MHC I complex / VP60-1 | ||||||
Function / homology | ![]() calicivirin / host cell endoplasmic reticulum / 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 / negative regulation of receptor binding / DAP12 interactions ...calicivirin / host cell endoplasmic reticulum / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / viral capsid / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / nucleoside-triphosphate phosphatase / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / RNA helicase activity / learning or memory / immune response / RNA-directed RNA polymerase / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / viral RNA genome replication / lysosomal membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / signaling receptor binding / 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 / RNA binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.4 KB | Display | ![]() |
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PDB format | ![]() | 71.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6m24C ![]() 6m2kC ![]() 5degS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31676.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1030.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M imidazole (pH 7.0), 12% w/v polyethylene glycol 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SDMS / Detector: CMOS / Date: Jun 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 29903 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 2.41 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.955 / Num. unique obs: 29903 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DEG Resolution: 2.2→47.28 Å / SU ML: 0.3037 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 27.667
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.28 Å
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Refine LS restraints |
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LS refinement shell |
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