+Open data
-Basic information
Entry | Database: PDB / ID: 7wbg | ||||||
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Title | BF2*1901/RY8 | ||||||
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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / 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 / 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: 2 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 | 7wbg.cif.gz | 212 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wbg.ent.gz | 135.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wbg_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 7wbg_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 7wbg_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 7wbg_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wbg ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wbg | HTTPS FTP |
-Related structure data
Related structure data | 7wbiC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30801.967 Da / Num. of mol.: 2 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 #2: Protein | Mass: 11062.404 Da / Num. of mol.: 2 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: 1126.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples) #4: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.15 M Potassium bromide and 30% 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: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 49775 / % possible obs: 98.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.142 / Num. unique obs: 4913 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YEZ Resolution: 2→33.4 Å / SU ML: 0.202 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.7077 / 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: 27.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.4 Å
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Refine LS restraints |
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LS refinement shell |
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