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- PDB-3i6l: Newly identified epitope N1 derived from SARS-CoV N protein compl... -
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Basic information
Entry | Database: PDB / ID: 3i6l | ||||||
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Title | Newly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402 | ||||||
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![]() | IMMUNE SYSTEM / HLA-A*2402 / SARS-CoV / nucleocapsid protein / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Golgi apparatus / Phosphoprotein / Ribonucleoprotein / RNA-binding / Viral nucleoprotein / Virion | ||||||
Function / homology | ![]() SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / 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 / SARS-CoV-1 modulates host translation machinery / endoplasmic reticulum exit site / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / SARS-CoV-1 activates/modulates innate immune responses / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / viral capsid / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / antibacterial humoral response / T cell differentiation in thymus / protein refolding / host cell Golgi apparatus / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / molecular adaptor activity / learning or memory / host cell perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, J.W. | ||||||
![]() | ![]() Title: Novel immunodominant peptide presentation strategy: a featured HLA-A*2402-restricted cytotoxic T-lymphocyte epitope stabilized by intrachain hydrogen bonds from severe acute respiratory ...Title: Novel immunodominant peptide presentation strategy: a featured HLA-A*2402-restricted cytotoxic T-lymphocyte epitope stabilized by intrachain hydrogen bonds from severe acute respiratory syndrome coronavirus nucleocapsid protein Authors: Liu, J. / Wu, P. / Gao, F. / Qi, J. / Kawana-Tachikawa, A. / Xie, J. / Vavricka, C.J. / Iwamoto, A. / Li, T. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 443.1 KB | Display | ![]() |
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Full document | ![]() | 449.8 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bckS 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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Unit cell |
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Components
#1: Protein | Mass: 31551.889 Da / Num. of mol.: 1 / Fragment: alpha 1-3 regions, UNP residues 25-298 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: 1090.292 Da / Num. of mol.: 1 / Fragment: UNP residue 346-354 / Source method: obtained synthetically / Details: chemical synthesized / Source: (synth.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.9, 25% 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: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→28.94 Å / Num. obs: 22272 / % possible obs: 98.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 40.671 / Num. measured all: 149410 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 6.211 / Num. unique all: 2166 / Rsym value: 0.387 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BCK Resolution: 2.4→28.94 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.68 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.465 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→28.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.398→2.46 Å / Total num. of bins used: 20
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