+Open data
-Basic information
Entry | Database: PDB / ID: 6ism | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of intracellular B30.2 domain of BTN3A1 mutant | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ism.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ism.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 6ism.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6ism ftp://data.pdbj.org/pub/pdb/validation_reports/is/6ism | HTTPS FTP |
---|
-Related structure data
Related structure data | 5zxkC 5zz3C 6itaC 6j06C 6j0gC 6j0kC 6j0lC 4n7uS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22504.562 Da / Num. of mol.: 1 / Fragment: UNP residues 328-513 / Mutation: W302A, L306A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O00481 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.21 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Magnesium chloride hexahydrate, HEPES pH 7.5, Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→41.14 Å / Num. obs: 42394 / % possible obs: 97.99 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 53.69 |
Reflection shell | Resolution: 1.25→1.29 Å / Rmerge(I) obs: 0.288 / Num. unique obs: 3880 / CC1/2: 0.914 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7U Resolution: 1.25→41.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.709 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.721 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.25→41.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|