+Open data
-Basic information
Entry | Database: PDB / ID: 8j9q | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of UBR box of UBR4 apo | ||||||||||||
Components | E3 ubiquitin-protein ligase UBR4 | ||||||||||||
Keywords | LIGASE / E3 ligase / UBR box | ||||||||||||
Function / homology | Function and homology information negative regulation of fatty acid biosynthetic process / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination ...negative regulation of fatty acid biosynthetic process / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / calmodulin binding / centrosome / Neutrophil degranulation / zinc ion binding / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||||||||
Authors | Jeong, D.-E. / KIm, S.-J. / Shin, H.-C. | ||||||||||||
Funding support | Korea, Republic Of, 3items
| ||||||||||||
Citation | Journal: Commun Biol / Year: 2023 Title: Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates. Authors: Jeong, D.E. / Lee, H.S. / Ku, B. / Kim, C.H. / Kim, S.J. / Shin, H.C. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8j9q.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8j9q.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 8j9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/8j9q ftp://data.pdbj.org/pub/pdb/validation_reports/j9/8j9q | HTTPS FTP |
---|
-Related structure data
Related structure data | 8j9rC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8238.634 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBR4, KIAA0462, KIAA1307, RBAF600, ZUBR1 / Production host: Escherichia coli (E. coli) References: UniProt: Q5T4S7, RING-type E3 ubiquitin transferase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.89 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1.283 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→29.76 Å / Num. obs: 15341 / % possible obs: 98.04 % / Redundancy: 12.7 % / Biso Wilson estimate: 40.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.99 |
Reflection shell | Resolution: 2.18→2.258 Å / Num. unique obs: 1490 / CC1/2: 0.926 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold Resolution: 2.18→29.76 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.6495 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→29.76 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|