+Open data
-Basic information
Entry | Database: PDB / ID: 7xf3 | ||||||
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Title | The structure of HLA-B*1501/BM58-66AF9 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complex / Peptide prensentation | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...viral budding from plasma membrane / 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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / 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 / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / membrane => GO:0016020 / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Influenza B virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Zhao, Y.Z. / Xiao, W.L. / Wu, Y.N. / Fan, W.F. / Yue, C. / Zhang, Q.X. / Zhang, D.N. / Yuan, X.J. / Yao, S.J. / Liu, S. ...Zhao, Y.Z. / Xiao, W.L. / Wu, Y.N. / Fan, W.F. / Yue, C. / Zhang, Q.X. / Zhang, D.N. / Yuan, X.J. / Yao, S.J. / Liu, S. / Li, M. / Wang, P.Y. / Zhang, H.J. / Zhang, J. / Zhao, M. / Zheng, X.Q. / Liu, W.J. / Gao, G.F. / Liu, W.L. | ||||||
Funding support | China, 1items
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Citation | Journal: J Immunol. / Year: 2023 Title: Parallel T Cell Immunogenic Regions in Influenza B and A Viruses with Distinct Nuclear Export Signal Functions: The Balance between Viral Life Cycle and Immune Escape. Authors: Zhao, Y. / Xiao, W. / Wu, Y. / Fan, W. / Li, L. / Yue, C. / Zhang, Q. / Zhang, D. / Yuan, X. / Yao, S. / Liu, S. / Li, M. / Wang, P. / Zhang, H. / Zhang, J. / Zhao, M. / Zheng, X. / Liu, W. ...Authors: Zhao, Y. / Xiao, W. / Wu, Y. / Fan, W. / Li, L. / Yue, C. / Zhang, Q. / Zhang, D. / Yuan, X. / Yao, S. / Liu, S. / Li, M. / Wang, P. / Zhang, H. / Zhang, J. / Zhao, M. / Zheng, X. / Liu, W. / Gao, G.F. / Liu, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xf3.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xf3.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/7xf3 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/7xf3 | HTTPS FTP |
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-Related structure data
Related structure data | 5txsS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31846.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: F4NBQ1 |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 894.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus / References: UniProt: Q71UK7 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% w/v PEG 2000, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 36034 / % possible obs: 98.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 17.71 Å2 / Rsym value: 0.1 / Net I/σ(I): 22.22 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 36034 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TXS Resolution: 1.91→30.7 Å / SU ML: 0.1898 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 22.3638 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→30.7 Å
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Refine LS restraints |
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LS refinement shell |
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