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Yorodumi- PDB-5wmq: Crystal Structure of HLA-B8 in complex with ELR, an Influenza A v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wmq | ||||||
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Title | Crystal Structure of HLA-B8 in complex with ELR, an Influenza A virus peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / viral peptide / IAV / EBV / CMV / crossreactivity / TCR / T cell / heterologous immunity | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule 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 / 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 / defense response / 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 / 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 / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / 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: 1.4 Å | ||||||
Authors | Gras, S. / Rossjohn, J. | ||||||
Citation | Journal: J. Immunol. / Year: 2018 Title: Inability To Detect Cross-Reactive Memory T Cells Challenges the Frequency of Heterologous Immunity among Common Viruses. Authors: Rowntree, L.C. / Nguyen, T.H.O. / Halim, H. / Purcell, A.W. / Rossjohn, J. / Gras, S. / Kotsimbos, T.C. / Mifsud, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wmq.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wmq.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 5wmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wmq_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 5wmq_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 5wmq_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5wmq_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/5wmq ftp://data.pdbj.org/pub/pdb/validation_reports/wm/5wmq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31930.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30460, UniProt: P01889*PLUS |
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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: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1195.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus |
#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: 2.41 Å3/Da / Density % sol: 48.99 % / Mosaicity: 0.28 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18-24%PEG4000, 0.2 NH4 Acetate, 0.1M Na-cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.4→43.82 Å / Num. obs: 82282 / % possible obs: 97 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.17 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 10.7 | |||||||||||||||||||||
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 / Resolution: 1.4→20.5 Å / Cor.coef. Fo:Fc: 0.9312 / Cor.coef. Fo:Fc free: 0.9243 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.065
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Displacement parameters | Biso mean: 19.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.4→20.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.44 Å / Total num. of bins used: 20
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