[English] 日本語
Yorodumi- PDB-4k55: Structure of the extracellular domain of butyrophilin BTN3A1 in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k55 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the extracellular domain of butyrophilin BTN3A1 in complex with (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP) | ||||||
Components | Butyrophilin subfamily 3 member A1 | ||||||
Keywords | SIGNALING PROTEIN / immunoglobulin superfamily | ||||||
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: 1.91 Å | ||||||
Authors | Kumar, A. / Mori, L. / De Libero, G. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2013 Title: Butyrophilin 3A1 binds phosphorylated antigens and stimulates human gamma delta T cells. Authors: Vavassori, S. / Kumar, A. / Wan, G.S. / Ramanjaneyulu, G.S. / Cavallari, M. / El Daker, S. / Beddoe, T. / Theodossis, A. / Williams, N.K. / Gostick, E. / Price, D.A. / Soudamini, D.U. / ...Authors: Vavassori, S. / Kumar, A. / Wan, G.S. / Ramanjaneyulu, G.S. / Cavallari, M. / El Daker, S. / Beddoe, T. / Theodossis, A. / Williams, N.K. / Gostick, E. / Price, D.A. / Soudamini, D.U. / Voon, K.K. / Olivo, M. / Rossjohn, J. / Mori, L. / De Libero, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4k55.cif.gz | 35 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4k55.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/4k55 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/4k55 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | One molecule in the asymmetric unit |
-Components
#1: Protein | Mass: 13772.517 Da / Num. of mol.: 1 / Fragment: unp residues 28-143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: BT3.2, BTF3, BTF4, BTF5, BTN3A1, BTN3A2, Butyrophilin subfamily 3 member A1 Plasmid: pET22b(+)-His6 / Production host: Escherichia coli (E. coli) / References: UniProt: O00481 |
---|---|
#2: Chemical | ChemComp-H6P / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.25 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.12 M ethylene glycols, 0.1 M buffer system 1, 30% PEG 550 MME and PEG 20,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→21.52 Å / Num. all: 18761 / Num. obs: 10398 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 19 / Num. unique all: 971 / % possible all: 97.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→21.52 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.894 / SU B: 3.083 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||
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 mean: 23.064 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→21.52 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.912→1.961 Å / Total num. of bins used: 20
|