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Open data
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Basic information
Entry | Database: PDB / ID: 6t0x | ||||||
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Title | Crystal structure of YTHDC1 with fragment 22 (ACA_DC1_001) | ||||||
![]() | YTHDC1 | ||||||
![]() | RNA BINDING PROTEIN / Fragment / Complex / YTHDC1 / Epitranscriptomic | ||||||
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. / Sledz, P. / Caflisch, A. | ||||||
![]() | ![]() Title: Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments. Authors: Bedi, R.K. / Huang, D. / Wiedmer, L. / Li, Y. / Dolbois, A. / Wojdyla, J.A. / Sharpe, M.E. / Caflisch, A. / Sledz, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.3 KB | Display | ![]() |
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PDB format | ![]() | 67.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6syzC ![]() 6sz1C ![]() 6sz2C ![]() 6sz3C ![]() 6sz7C ![]() 6sz8C ![]() 6szlC ![]() 6sznC ![]() 6szrC ![]() 6sztC ![]() 6szxC ![]() 6szyC ![]() 6t01C ![]() 6t02C ![]() 6t03C ![]() 6t04C ![]() 6t05C ![]() 6t06C ![]() 6t07C ![]() 6t08C ![]() 6t09C ![]() 6t0aC ![]() 6t0cC ![]() 6t0dC ![]() 6t0oC ![]() 6t0zC ![]() 6t10C ![]() 6t11C ![]() 6t12C ![]() 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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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 | #3: Chemical | ChemComp-SO4 / #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: 1.97 Å3/Da / Density % sol: 37.68 % |
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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-F / Detector: PIXEL / Date: Apr 14, 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→40.6 Å / Num. obs: 68687 / % possible obs: 99.1 % / Redundancy: 3.39 % / Biso Wilson estimate: 14.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.19 |
Reflection shell | Resolution: 1.36→1.45 Å / Num. unique obs: 10862 / CC1/2: 0.627 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4r3h Resolution: 1.36→40.59 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2425
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→40.59 Å
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Refine LS restraints |
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LS refinement shell |
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