+Open data
-Basic information
Entry | Database: PDB / ID: 8bs5 | ||||||
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Title | Crystal structure of YTHDF3 YTH domain open conformation | ||||||
Components | YTH domain-containing family protein 3 | ||||||
Keywords | RNA BINDING PROTEIN / YTHDF3 / 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: 2.49 Å | ||||||
Authors | Bedi, R.K. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of YTHDF3 YTH domain open conformation Authors: Bedi, R.K. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bs5.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bs5.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/8bs5 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/8bs5 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23099.037 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: Chemical | ChemComp-TLA / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2M Potassium sodium tartrate tetrahydrate, 20% PEG 3350 |
-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: Nov 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→48.73 Å / Num. obs: 14732 / % possible obs: 99.5 % / Redundancy: 12.81 % / Biso Wilson estimate: 35.3 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.23 |
Reflection shell | Resolution: 2.49→2.64 Å / Num. unique obs: 2250 / CC1/2: 0.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→41.77 Å / SU ML: 0.3204 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.0416 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: 42.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→41.77 Å
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Refine LS restraints |
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LS refinement shell |
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