+Open data
-Basic information
Entry | Database: PDB / ID: 6jbm | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the TRIM14 PRYSPRY domain | ||||||||||||
Components | Tripartite motif-containing protein 14 | ||||||||||||
Keywords | PROTEIN BINDING / TRIM / protein interaction domain | ||||||||||||
Function / homology | Function and homology information regulation of viral entry into host cell / negative regulation of viral transcription / positive regulation of autophagy / phagocytic vesicle / positive regulation of DNA-binding transcription factor activity / protein polyubiquitination / regulation of protein localization / Interferon gamma signaling / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity ...regulation of viral entry into host cell / negative regulation of viral transcription / positive regulation of autophagy / phagocytic vesicle / positive regulation of DNA-binding transcription factor activity / protein polyubiquitination / regulation of protein localization / Interferon gamma signaling / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / regulation of gene expression / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / transcription coactivator activity / protein ubiquitination / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Yin, Y.X. / Yu, Y. / Liang, L. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Febs Lett. / Year: 2019 Title: The TRIM14 PRYSPRY domain mediates protein interaction via its basic interface. Authors: Yu, Y. / Liang, L. / Jin, Y. / Yin, Y. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jbm.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jbm.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jbm_validation.pdf.gz | 482.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6jbm_full_validation.pdf.gz | 495.5 KB | Display | |
Data in XML | 6jbm_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 6jbm_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/6jbm ftp://data.pdbj.org/pub/pdb/validation_reports/jb/6jbm | HTTPS FTP |
-Related structure data
Related structure data | 4n7iS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22894.139 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM14, KIAA0129 / Plasmid: pet28a+ / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5[alpha] / References: UniProt: Q14142 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Ammonium sulfate, PEG8000 / PH range: 6.0-7.0 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 46284 / % possible obs: 99.4 % / Redundancy: 3.3 % / Net I/σ(I): 9.39 |
Reflection shell | Resolution: 2.1→2.15 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7I Resolution: 2.1→35.396 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.23
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→35.396 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|