[English] 日本語
Yorodumi- PDB-5www: Crystal structure of the KH1 domain of human RNA-binding E3 ubiqu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5www | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the KH1 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C complex with RNA | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN/RNA / KH1 / MEX-3C / RNA / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information chondrocyte hypertrophy / regulation of fat cell differentiation / energy homeostasis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / RNA binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Yang, L. / Wang, C. / Li, F. / Gong, Q. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity Authors: Yang, L. / Wang, C. / Li, F. / Zhang, J. / Nayab, A. / Wu, J. / Shi, Y. / Gong, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5www.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5www.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 5www.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/5www ftp://data.pdbj.org/pub/pdb/validation_reports/ww/5www | HTTPS FTP |
---|
-Related structure data
Related structure data | 5wwxC 5wwzC 2dgrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 10512.194 Da / Num. of mol.: 1 / Fragment: KH1 domain, UNP residues 221-306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MEX3C, RKHD2, RNF194, BM-013 / Production host: Escherichia coli (E. coli) References: UniProt: Q5U5Q3, RING-type E3 ubiquitin transferase |
---|---|
#2: RNA chain | Mass: 1893.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 5% v/v Tacsimate pH 7.0, 0.1M HEPES pH 7.0, 10% w/v polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→40 Å / Num. obs: 11406 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 22.96 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.053 / Rrim(I) all: 0.168 / Χ2: 1.051 / Net I/σ(I): 3.6 / Num. measured all: 115295 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DGR Resolution: 1.798→38.183 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.37 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.34 Å2 / Biso mean: 26.3348 Å2 / Biso min: 11.63 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.798→38.183 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
|