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Yorodumi- PDB-8bs6: Crystal structure of YTHDF3 disulfide mutant (closed conformation) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bs6 | ||||||
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Title | Crystal structure of YTHDF3 disulfide mutant (closed conformation) | ||||||
Components | YTH domain-containing family protein 3 | ||||||
Keywords | RNA BINDING PROTEIN / YTHDF3 / mutant / disulfide / YTH / m6A | ||||||
Function / homology | Function and homology information organelle assembly / regulation of trophoblast cell migration / N6-methyladenosine-containing RNA reader activity / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability / positive regulation of translation / P-body ...organelle assembly / regulation of trophoblast cell migration / N6-methyladenosine-containing RNA reader activity / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability / positive regulation of translation / P-body / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Bedi, R.K. / Li, Y. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of YTHDF3 disulfide mutant (closed conformation) Authors: Bedi, R.K. / Li, Y. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bs6.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bs6.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/8bs6 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/8bs6 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25507.803 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z739 |
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#2: 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: 1.78 Å3/Da / Density % sol: 30.74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 2M Disodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→44.83 Å / Num. obs: 55256 / % possible obs: 100 % / Redundancy: 8.36 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.83 |
Reflection shell | Resolution: 1.2→1.27 Å / Num. unique obs: 8867 / CC1/2: 0.799 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→32.52 Å / SU ML: 0.131 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5013 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→32.52 Å
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Refine LS restraints |
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LS refinement shell |
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