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Yorodumi- PDB-7jyw: Crystal Structure of HLA A*2402 in complex with TYQWIIRNW, an 9-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jyw | |||||||||
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Title | Crystal Structure of HLA A*2402 in complex with TYQWIIRNW, an 9-mer influenza epitope | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA A*2402 / influenza virus / TCR / T cell | |||||||||
Function / homology | Function and homology information 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 ...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 / 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 / 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 / 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 / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | |||||||||
Authors | Gras, S. / Nguyen, A.T. / Szeto, C. / Rossjohn, J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: CD8 + T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph. Authors: Hensen, L. / Illing, P.T. / Bridie Clemens, E. / Nguyen, T.H.O. / Koutsakos, M. / van de Sandt, C.E. / Mifsud, N.A. / Nguyen, A.T. / Szeto, C. / Chua, B.Y. / Halim, H. / Rizzetto, S. / ...Authors: Hensen, L. / Illing, P.T. / Bridie Clemens, E. / Nguyen, T.H.O. / Koutsakos, M. / van de Sandt, C.E. / Mifsud, N.A. / Nguyen, A.T. / Szeto, C. / Chua, B.Y. / Halim, H. / Rizzetto, S. / Luciani, F. / Loh, L. / Grant, E.J. / Saunders, P.M. / Brooks, A.G. / Rockman, S. / Kotsimbos, T.C. / Cheng, A.C. / Richards, M. / Westall, G.P. / Wakim, L.M. / Loudovaris, T. / Mannering, S.I. / Elliott, M. / Tangye, S.G. / Jackson, D.C. / Flanagan, K.L. / Rossjohn, J. / Gras, S. / Davies, J. / Miller, A. / Tong, S.Y.C. / Purcell, A.W. / Kedzierska, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jyw.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jyw.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 7jyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/7jyw ftp://data.pdbj.org/pub/pdb/validation_reports/jy/7jyw | HTTPS FTP |
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-Related structure data
Related structure data | 6xqaC 7jyuC 7jyvC 7jyxC 4f7mS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31952.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411J078 |
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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, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1280.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide from influenza virus / Source: (synth.) Influenza A virus |
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-Non-polymers , 4 types, 18 molecules
#4: Chemical | ChemComp-CA / | ||||
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#5: Chemical | #6: Chemical | ChemComp-NI / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 3.81 Å3/Da / Density % sol: 67.71 % / Mosaicity: 0.05 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 20% PEG3350, 0.2M Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.98 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.9→48.16 Å / Num. obs: 16623 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 93.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.4 / Num. measured all: 159459 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F7M Resolution: 2.9→48.16 Å / Cor.coef. Fo:Fc: 0.833 / Cor.coef. Fo:Fc free: 0.819 / SU R Cruickshank DPI: 0.635 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.703 / SU Rfree Blow DPI: 0.351 / SU Rfree Cruickshank DPI: 0.349
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Displacement parameters | Biso max: 191.19 Å2 / Biso mean: 108.4 Å2 / Biso min: 66.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→48.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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