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Yorodumi- PDB-6j0g: Crystal structure of intracellular B30.2 domain of BTN3A3 mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j0g | ||||||
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Title | Crystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with HMBPP | ||||||
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: 1.6 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 | 6j0g.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0g.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 6j0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0g ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0g | HTTPS FTP |
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-Related structure data
Related structure data | 5zxkC 5zz3C 6ismC 6itaC 6j06C 6j0kC 6j0lC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25272.418 Da / Num. of mol.: 4 / 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) / References: UniProt: O00478 #2: Chemical | ChemComp-H6P / ( #3: 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: 1.95 Å3/Da / Density % sol: 36.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Sodium Acetate trihydrate , Tris Hydrochloride ,Polyethylene Glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 97578 / % possible obs: 96.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.11 |
Reflection shell | Resolution: 1.6→1.66 Å / Num. unique obs: 9312 / CC1/2: 0.951 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7U Resolution: 1.6→24.685 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 37.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→24.685 Å
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Refine LS restraints |
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LS refinement shell |
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