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Yorodumi- PDB-3i6k: Newly identified epitope from SARS-CoV membrane protein complexed... -
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-Basic information
Entry | Database: PDB / ID: 3i6k | ||||||
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Title | Newly identified epitope from SARS-CoV membrane protein complexed with HLA-A*0201 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA-A2 / SARS-CoV / Membrane glycoprotein / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Envelope protein / Golgi apparatus / Viral matrix protein / Virion | ||||||
Function / homology | Function and homology information Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation ...Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / 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 / positive regulation of type II interferon production / 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 / SARS-CoV-1 activates/modulates innate immune responses / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / structural constituent of virion / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) SARS coronavirus TJF | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liu, J. / Sun, Y. / Qi, J. / Chu, F. / Wu, H. / Gao, F. / Li, T. / Yan, J. / Gao, G.F. | ||||||
Citation | Journal: J Infect Dis / Year: 2010 Title: The membrane protein of severe acute respiratory syndrome coronavirus acts as a dominant immunogen revealed by a clustering region of novel functionally and structurally defined cytotoxic T-lymphocyte epitopes Authors: Liu, J. / Sun, Y. / Qi, J. / Chu, F. / Wu, H. / Gao, F. / Li, T. / Yan, J. / 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 | 3i6k.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i6k.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i6k_validation.pdf.gz | 463.2 KB | Display | wwPDB validaton report |
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Full document | 3i6k_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | 3i6k_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 3i6k_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i6k ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i6k | HTTPS FTP |
-Related structure data
Related structure data | 3i6gC 1jf1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: alpha 1-3 regions, UNP residues 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: HLA-A, HLA-A*0201 allele, HLAA, Homo sapiens MHC class I antigen (HLA-A) Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, beta-2-microglobulin, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1007.246 Da / Num. of mol.: 2 / Fragment: UNP residue 60-69 / Source method: obtained synthetically / Details: chemical synthesized / Source: (synth.) SARS coronavirus TJF / References: UniProt: Q692E0, UniProt: P59596*PLUS #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: 2.67 Å3/Da / Density % sol: 53.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M BIS-TRIS pH 5.5, 10% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 14, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av R equivalents: 0.17 / Number: 173044 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→32.209 Å / Num. obs: 25460 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.17 / Rrim(I) all: 0.17 / Rsym value: 0.17 / Χ2: 2.156 / Net I/σ(I): 15.836 / Num. measured all: 173044 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Cell measurement | Reflection used: 173044 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JF1 Resolution: 2.8→32.209 Å / Occupancy max: 1 / Occupancy min: 0.61 / FOM work R set: 0.845 / SU ML: 0.29 / σ(F): 0.11 / Phase error: 22.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.509 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.13 Å2 / Biso mean: 35.595 Å2 / Biso min: 12.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→32.209 Å
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Refine LS restraints |
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LS refinement shell |
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