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Yorodumi- PDB-5wwx: Crystal structure of the KH2 domain of human RNA-binding E3 ubiqu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wwx | ||||||
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Title | Crystal structure of the KH2 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C complex with RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / KH2 / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wwx.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wwx.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wwx_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 5wwx_full_validation.pdf.gz | 444.2 KB | Display | |
Data in XML | 5wwx_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 5wwx_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/5wwx ftp://data.pdbj.org/pub/pdb/validation_reports/ww/5wwx | HTTPS FTP |
-Related structure data
Related structure data | 5wwwSC 5wwzC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9772.222 Da / Num. of mol.: 1 / Fragment: KH2 domain, UNP residues 320-396 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 |
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#2: RNA chain | Mass: 1610.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-NI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.04M Magnesium acetate tetrahydrate, 0.05M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 2→40 Å / Num. obs: 6609 / % possible obs: 99.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 23.13 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 3.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WWW Resolution: 2→33.367 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 106.81 Å2 / Biso mean: 23.0942 Å2 / Biso min: 8.76 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→33.367 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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