+Open data
-Basic information
Entry | Database: PDB / ID: 7wbi | ||||||
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Title | BF2*1901-FLU | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC I | ||||||
Function / homology | Function and homology information ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / 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 / 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 / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / membrane / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) uncultured virus (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, W.J. | ||||||
Funding support | China, 1items
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Citation | Journal: J Immunol. / Year: 2023 Title: A Wider and Deeper Peptide-Binding Groove for the Class I Molecules from B15 Compared with B19 Chickens Correlates with Relative Resistance to Marek's Disease. Authors: Han, L. / Wu, S. / Zhang, T. / Peng, W. / Zhao, M. / Yue, C. / Wen, W. / Cai, W. / Li, M. / Wallny, H.J. / Avila, D.W. / Mwangi, W. / Nair, V. / Ternette, N. / Guo, Y. / Zhao, Y. / Chai, Y. ...Authors: Han, L. / Wu, S. / Zhang, T. / Peng, W. / Zhao, M. / Yue, C. / Wen, W. / Cai, W. / Li, M. / Wallny, H.J. / Avila, D.W. / Mwangi, W. / Nair, V. / Ternette, N. / Guo, Y. / Zhao, Y. / Chai, Y. / Qi, J. / Liang, H. / Gao, G.F. / Kaufman, J. / 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 | 7wbi.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wbi.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 7wbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wbi_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 7wbi_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 7wbi_validation.xml.gz | 20 KB | Display | |
Data in CIF | 7wbi_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wbi ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wbi | HTTPS FTP |
-Related structure data
Related structure data | 7wbgC 2yezS S: Starting model for refinement C: citing same article (ref.) |
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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: 30801.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: BF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ZXM5 |
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#2: Protein | Mass: 11062.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P21611 |
#3: Protein/peptide | Mass: 1170.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples) |
#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: 2.18 Å3/Da / Density % sol: 43.66 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M BIS-TRIS pH 6.5 and 28% w/v Polyethylene glycol monomethyl ether 2,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU / Detector: PIXEL / Date: Jun 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35678 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 16.36 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.207 / Num. unique obs: 35671 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YEZ Resolution: 1.8→35.71 Å / SU ML: 0.1604 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 18.7213 / 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: 19.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.71 Å
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Refine LS restraints |
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LS refinement shell |
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