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Open data
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Basic information
Entry | Database: PDB / ID: 6yni | ||||||
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Title | Crystal structure of YTHDC1 with compound DHU_DC1_036 | ||||||
![]() | YTHDC1 | ||||||
![]() | RNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor | ||||||
Function / homology | ![]() primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bedi, R.K. / Huang, D. / Wiedmer, L. / Caflisch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based design of ligands of the m6A-RNA reader YTHDC1 Authors: Li, Y. / Bedi, R.K. / Nai, F. / von Roten, V. / Dolbois, A. / Zalesak, F. / Nachawati, R. / Huang, D. / Caflisch, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.7 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ykeC ![]() 6ykiC ![]() 6ykjC ![]() 6ykzC ![]() 6yl8C ![]() 6yl9C ![]() 6ynjC ![]() 6ynkC ![]() 6ynlC ![]() 6ynmC ![]() 6ynpC ![]() 6yoqC ![]() 7p87C ![]() 7p88C ![]() 7p8aC ![]() 7p8bC ![]() 7p8fC ![]() 7pj7C ![]() 7pj8C ![]() 7pj9C ![]() 7pjaC ![]() 7pjbC ![]() 7pjpC ![]() 7pjqC ![]() 4r3hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20967.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→40.3 Å / Num. obs: 67741 / % possible obs: 99.2 % / Redundancy: 2.97 % / Biso Wilson estimate: 15.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 1.36→1.44 Å / Num. unique obs: 10880 / CC1/2: 0.658 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4r3h Resolution: 1.36→40.3 Å / SU ML: 0.1609 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.9458 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→40.3 Å
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Refine LS restraints |
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LS refinement shell |
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