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Yorodumi- PDB-5nq3: 'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, ... -
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-Basic information
Entry | Database: PDB / ID: 5nq3 | ||||||
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Title | 'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting EFEDLTFLA | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / CD8+ / influenza / swine / SLA | ||||||
Function / homology | Function and homology information cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / antigen processing and presentation of peptide antigen via MHC class I / Viral Messenger RNA Synthesis / vRNP Assembly / helical viral capsid / Viral mRNA Translation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / viral penetration into host nucleus / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / ribonucleoprotein complex / symbiont entry into host cell / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Homo sapiens (human) unidentified influenza virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å | ||||||
Authors | Rizkallah, P.J. / Tungatt, K. / Sewell, A.K. | ||||||
Citation | Journal: Plos Pathog. / Year: 2018 Title: Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig. Authors: Tungatt, K. / Dolton, G. / Morgan, S.B. / Attaf, M. / Fuller, A. / Whalley, T. / Hemmink, J.D. / Porter, E. / Szomolay, B. / Montoya, M. / Hammond, J.A. / Miles, J.J. / Cole, D.K. / ...Authors: Tungatt, K. / Dolton, G. / Morgan, S.B. / Attaf, M. / Fuller, A. / Whalley, T. / Hemmink, J.D. / Porter, E. / Szomolay, B. / Montoya, M. / Hammond, J.A. / Miles, J.J. / Cole, D.K. / Townsend, A. / Bailey, M. / Rizkallah, P.J. / Charleston, B. / Tchilian, E. / Sewell, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nq3.cif.gz | 344.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nq3.ent.gz | 282.2 KB | Display | PDB format |
PDBx/mmJSON format | 5nq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/5nq3 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/5nq3 | HTTPS FTP |
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-Related structure data
Related structure data | 5npzC 5nq0C 5nq1C 5nq2C 5qq3S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 31678.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PJV3 #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, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 1084.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: P03466*PLUS |
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-Non-polymers , 4 types, 801 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: 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: 2.27 Å3/Da / Density % sol: 45.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: JBS screen, condition A07: 30% MPD, 100 mM Na Citrate, pH 5.6, 200 mM Ammonium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→61.44 Å / Num. obs: 105240 / % possible obs: 96 % / Redundancy: 1.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.57→1.61 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.665 / % possible all: 93.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5QQ3 Resolution: 1.57→61.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.374 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.115 / 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: 26.823 Å2
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Refinement step | Cycle: 1 / Resolution: 1.57→61.44 Å
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Refine LS restraints |
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