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Yorodumi- PDB-8ixv: Crystal structure of intracellular B30.2 domain of BTN3A in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ixv | ||||||
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Title | Crystal structure of intracellular B30.2 domain of BTN3A in complex with 2Cl-HMBPP | ||||||
Components | Butyrophilin subfamily 3 member A1 | ||||||
Keywords | SIGNALING PROTEIN / Butyrophilin | ||||||
Function / homology | Function and homology information Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Yang, Y.Y. / Yi, S.M. / 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 | 8ixv.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ixv.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ixv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/8ixv ftp://data.pdbj.org/pub/pdb/validation_reports/ix/8ixv | HTTPS FTP |
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-Related structure data
Related structure data | 8hjtC 8igtC 8ih4C 8izeC 8izgC 8jy9C 8jyaC 8jybC 8jycC 8jyeC 8jyfC 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: 22661.773 Da / Num. of mol.: 1 / Fragment: UNP residues 328-513 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00481 |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-RZO / [ |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: Calcium acetate hydrate, PEG8000,Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Mar 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→45.77 Å / Num. obs: 23485 / % possible obs: 98.9 % / Redundancy: 8.46 % / Biso Wilson estimate: 20.55 Å2 / Rmerge(I) obs: 0.0482 / Net I/σ(I): 24.96 |
Reflection shell | Resolution: 1.72→1.82 Å / Rmerge(I) obs: 0.2179 / Num. unique obs: 1167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→32.21 Å / SU ML: 0.2105 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2345 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→32.21 Å
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Refine LS restraints |
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LS refinement shell |
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