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Yorodumi- PDB-6j0l: Crystal structure of intracellular B30.2 domain of BTN3A3 mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j0l | ||||||
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Title | Crystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with sulfate ion | ||||||
Components | Butyrophilin subfamily 3 member A3 | ||||||
Keywords | SIGNALING PROTEIN / Butyrophilin | ||||||
Function / homology | Function and homology information Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / T cell receptor signaling pathway / external side of plasma membrane / signaling receptor binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Yang, Y.Y. / Liu, W.D. / Cai, N.N. / Chen, C.C. / Guo, R.T. / Zhang, Y.H. | ||||||
Citation | Journal: Immunity / Year: 2019 Title: A Structural Change in Butyrophilin upon Phosphoantigen Binding Underlies Phosphoantigen-Mediated V gamma 9V delta 2 T Cell Activation. Authors: Yang, Y. / Li, L. / Yuan, L. / Zhou, X. / Duan, J. / Xiao, H. / Cai, N. / Han, S. / Ma, X. / Liu, W. / Chen, C.C. / Wang, L. / Li, X. / Chen, J. / Kang, N. / Chen, J. / Shen, Z. / Malwal, S. ...Authors: Yang, Y. / Li, L. / Yuan, L. / Zhou, X. / Duan, J. / Xiao, H. / Cai, N. / Han, S. / Ma, X. / Liu, W. / Chen, C.C. / Wang, L. / Li, X. / Chen, J. / Kang, N. / Chen, J. / Shen, Z. / Malwal, S.R. / Liu, W. / Shi, Y. / 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 | 6j0l.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0l.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 6j0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0l ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0l | HTTPS FTP |
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-Related structure data
Related structure data | 5zxkC 5zz3C 6ismC 6itaC 6j06C 6j0gC 6j0kC 4n7uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25272.418 Da / Num. of mol.: 2 / Fragment: UNP residues 328-515 / Mutation: R351H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A3, BTF3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00478 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | The intracellular B30.2 domain of BTN3A3 was redesigned to have TEV protease cleavage sites and ...The intracellular B30.2 domain of BTN3A3 was redesigned to have TEV protease cleavage sites and bordering the linker region(AGAGA). | |
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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: 2.03 Å3/Da / Density % sol: 39.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: BIS-TRIS ,Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 28751 / % possible obs: 97.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.37 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 2900 / CC1/2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7U Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.813 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.728 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→25 Å
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Refine LS restraints |
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