[English] 日本語
![](img/lk-miru.gif)
- PDB-6rt5: The YTH domain of YTHDC1 protein in complex with Gm6AC oligonucleotide -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6rt5 | ||||||
---|---|---|---|---|---|---|---|
Title | The YTH domain of YTHDC1 protein in complex with Gm6AC oligonucleotide | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN / Protein-RNA interaction / epitranscriptomics | ||||||
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. / Sledz, P. / Caflisch, A. | ||||||
![]() | ![]() Title: Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif. Authors: Li, Y. / Bedi, R.K. / Wiedmer, L. / Huang, D. / Sledz, P. / Caflisch, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 83.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 476.9 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rt4C ![]() 6rt6C ![]() 6rt7C ![]() 4r3hS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 948.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Protein | Mass: 18823.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 0.1 M Bis-Tris at pH 6.5, 0.2 M ammonium sulfate and 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000002 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40.41 Å / Num. obs: 14246 / % possible obs: 97.8 % / Redundancy: 4.48 % / CC1/2: 0.999 / Rrim(I) all: 0.043 / Net I/σ(I): 26.26 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 4.5 % / Num. unique obs: 2119 / CC1/2: 0.988 / Rrim(I) all: 0.147 / % possible all: 91.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4R3H Resolution: 2.303→40.4 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.87
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.303→40.4 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|