+Open data
-Basic information
Entry | Database: PDB / ID: 4j0u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of IFIT5/ISG58 | ||||||
Components | Interferon-induced protein with tetratricopeptide repeats 5 | ||||||
Keywords | RNA BINDING PROTEIN / IFIT5 structure / helix / antiviral | ||||||
Function / homology | Function and homology information RNA cap binding / poly(U) RNA binding / negative regulation of viral genome replication / ruffle membrane / Interferon alpha/beta signaling / actin cytoskeleton / apical part of cell / double-stranded DNA binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus ...RNA cap binding / poly(U) RNA binding / negative regulation of viral genome replication / ruffle membrane / Interferon alpha/beta signaling / actin cytoskeleton / apical part of cell / double-stranded DNA binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / tRNA binding / single-stranded RNA binding / innate immune response / RNA binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.969 Å | ||||||
Authors | Liu, Y. / Liang, H. / Feng, F. / Yuan, L. / Wang, Y.E. / Crowley, C. / Lv, Z. / Li, J. / Zeng, S. / Cheng, G. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of IFIT5 Authors: Liu, Y. / Liang, H. / Feng, F. / Yuan, L. / Wang, Y.E. / Crowley, C. / Lv, Z. / Li, J. / Zeng, S. / Cheng, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4j0u.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4j0u.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 4j0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/4j0u ftp://data.pdbj.org/pub/pdb/validation_reports/j0/4j0u | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55933.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFIT5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13325 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.74 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100mM HEPES, 150mM NaCl, 8% PEG3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.969→50 Å / Num. all: 37989 / Num. obs: 37930 / % possible obs: 99 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 4.8 / Biso Wilson estimate: 28.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.969→36.725 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.835 / SU ML: 0.23 / σ(F): 0 / Phase error: 23.16 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.666 Å2 / ksol: 0.348 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.84 Å2 / Biso mean: 39.7091 Å2 / Biso min: 15.66 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.969→36.725 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|