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Yorodumi- PDB-6xqa: Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xqa | |||||||||
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Title | Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from Influenza B virus | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA-A*2402 / influenza virus B / IBV / 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 / early endosome membrane / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / focal adhesion / signaling receptor binding / 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 B virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å | |||||||||
Authors | Nguyen, A.T. / Szeto, C. / Gras, S. | |||||||||
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 | 6xqa.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xqa.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xqa_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 6xqa_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 6xqa_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 6xqa_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/6xqa ftp://data.pdbj.org/pub/pdb/validation_reports/xq/6xqa | HTTPS FTP |
-Related structure data
Related structure data | 7jyuC 7jyvC 7jywC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31952.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411J078 #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 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1165.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: influenza virus / Source: (synth.) Influenza B virus #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.65 Å3/Da / Density % sol: 53.6 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 24% PEG8000, 0.1 HEPES pH 7.5, 2% isopropanol, 5% w/v Polyvinylpyrrolidone K15 |
-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: Feb 19, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.16→44.81 Å / Num. obs: 49524 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.4 / Num. measured all: 188348 / Scaling rejects: 7 | ||||||||||||||||||||||||
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: 2.16→44.81 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.185
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Displacement parameters | Biso max: 126.55 Å2 / Biso mean: 35.14 Å2 / Biso min: 3.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.16→44.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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