+Open data
-Basic information
Entry | Database: PDB / ID: 6l9u | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse TIFA | |||||||||
Components | TRAF-interacting protein with FHA domain-containing protein A | |||||||||
Keywords | SIGNALING PROTEIN / FHA domain | |||||||||
Function / homology | Function and homology information Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / cytoplasmic pattern recognition receptor signaling pathway / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / protein homooligomerization / positive regulation of canonical NF-kappaB signal transduction / innate immune response / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å | |||||||||
Authors | Nakamura, T. / Yamagata, Y. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate immunity. Authors: Nakamura, T. / Hashikawa, C. / Okabe, K. / Yokote, Y. / Chirifu, M. / Toma-Fukai, S. / Nakamura, N. / Matsuo, M. / Kamikariya, M. / Okamoto, Y. / Gohda, J. / Akiyama, T. / Semba, K. / ...Authors: Nakamura, T. / Hashikawa, C. / Okabe, K. / Yokote, Y. / Chirifu, M. / Toma-Fukai, S. / Nakamura, N. / Matsuo, M. / Kamikariya, M. / Okamoto, Y. / Gohda, J. / Akiyama, T. / Semba, K. / Ikemizu, S. / Otsuka, M. / Inoue, J.I. / Yamagata, Y. #1: Journal: To Be Published Title: Crystallization and preliminary X-ray analysis of mouse TIFA Authors: Nakamura, T. / Inoue, J. / Yamagata, Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6l9u.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6l9u.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 6l9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/6l9u ftp://data.pdbj.org/pub/pdb/validation_reports/l9/6l9u | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22651.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tifa, T2bp / Production host: Escherichia coli (E. coli) / References: UniProt: Q793I8 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: MES pH 6.4, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.43 Å / Num. obs: 6561 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 48.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.636 / Num. unique obs: 331 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.601→45.429 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.84
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.77 Å2 / Biso mean: 81.6295 Å2 / Biso min: 38.29 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.601→45.429 Å
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 14.8152 Å / Origin y: 14.9041 Å / Origin z: 50.6647 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain A |