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Yorodumi- PDB-8jy9: Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jy9 | ||||||
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Title | Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with HMBPP | ||||||
Components | Butyrophylin 3 | ||||||
Keywords | SIGNALING PROTEIN / Butyrophilin | ||||||
Function / homology | Function and homology information regulation of cytokine production / T cell receptor signaling pathway / external side of plasma membrane / signaling receptor binding Similarity search - Function | ||||||
Biological species | Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Yang, Y.Y. / Yi, S.M. / Zhang, M.T. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2023 Title: Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate V gamma 9V delta 2 T cells. Authors: Yuan, L. / Ma, X. / Yang, Y. / Qu, Y. / Li, X. / Zhu, X. / Ma, W. / Duan, J. / Xue, J. / Yang, H. / Huang, J.W. / Yi, S. / Zhang, M. / Cai, N. / Zhang, L. / Ding, Q. / Lai, K. / Liu, C. / ...Authors: Yuan, L. / Ma, X. / Yang, Y. / Qu, Y. / Li, X. / Zhu, X. / Ma, W. / Duan, J. / Xue, J. / Yang, H. / Huang, J.W. / Yi, S. / Zhang, M. / Cai, N. / Zhang, L. / Ding, Q. / Lai, K. / Liu, C. / Zhang, L. / Liu, X. / Yao, Y. / Zhou, S. / Li, X. / Shen, P. / Chang, Q. / Malwal, S.R. / He, Y. / Li, W. / Chen, C. / Chen, C.C. / Oldfield, E. / Guo, R.T. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jy9.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jy9.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jy9_validation.pdf.gz | 1012.5 KB | Display | wwPDB validaton report |
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Full document | 8jy9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8jy9_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 8jy9_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/8jy9 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/8jy9 | HTTPS FTP |
-Related structure data
Related structure data | 8hjtC 8igtC 8ih4C 8ixvC 8izeC 8izgC 8jyaC 8jybC 8jycC 8jyeC 8jyfC 5zxkS 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: 22482.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: Btn3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A345DF50 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.22 Å3/Da / Density % sol: 44.54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis Tris pH 5.5, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Feb 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→37.39 Å / Num. obs: 36047 / % possible obs: 99.6 % / Redundancy: 10.07 % / Rmerge(I) obs: 0.1228 / Net I/σ(I): 13.45 |
Reflection shell | Resolution: 1.83→1.86 Å / Rmerge(I) obs: 0.4812 / Num. unique obs: 1632 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZXK Resolution: 1.83→37.39 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.901 / SU B: 3.868 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.54 Å2 / Biso mean: 17.851 Å2 / Biso min: 5.19 Å2
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Refinement step | Cycle: final / Resolution: 1.83→37.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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