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Open data
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Basic information
Entry | Database: PDB / ID: 7r5l | ||||||
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Title | Crystal structure of YTHDF2 with compound YLI_DC1_015 | ||||||
![]() | YTH domain-containing family protein 2 | ||||||
![]() | RNA BINDING PROTEIN / Epitranscriptomic reader m6A reader | ||||||
Function / homology | ![]() C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / regulation of rRNA processing / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / gamete generation / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity ...C5-methylcytidine-containing RNA reader activity / organelle assembly / spermatogonial cell division / regulation of meiotic cell cycle process involved in oocyte maturation / regulation of rRNA processing / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / gamete generation / embryonic morphogenesis / N6-methyladenosine-containing RNA reader activity / negative regulation of stem cell differentiation / oocyte maturation / regulation of hematopoietic stem cell differentiation / hematopoietic stem cell proliferation / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / humoral immune response / centriolar satellite / regulation of neurogenesis / regulation of cell adhesion / stress granule assembly / regulation of mRNA stability / P-body / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / cell cycle / innate immune response / mRNA binding / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nachawati, R. / Nai, F. / Li, Y. / Caflisch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Fragment Ligands of the m 6 A-RNA Reader YTHDF2. Authors: Nai, F. / Nachawati, R. / Zalesak, F. / Wang, X. / Li, Y. / 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 | ![]() | 57.9 KB | Display | ![]() |
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PDB format | ![]() | 33 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 732.1 KB | Display | ![]() |
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Full document | ![]() | 732.1 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r5fC ![]() 7r5wC ![]() 7ywbC ![]() 7yx6C ![]() 7yxeC ![]() 7z26C ![]() 7z4uC ![]() 7z54C ![]() 7z5mC ![]() 7z7bC ![]() 7z7fC ![]() 7z8pC ![]() 7z8wC ![]() 7z8xC ![]() 7z92C ![]() 7z93C ![]() 7zg4C ![]() 4rdnS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19367.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-I4S / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 1.95 M Ammonium sulfate, 0.1 M Sodium citrate tribasic pH 5.0 |
-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: Aug 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.12 Å / Num. obs: 22678 / % possible obs: 99.8 % / Redundancy: 19.68 % / Biso Wilson estimate: 21.57 Å2 / CC1/2: 1 / Net I/σ(I): 26.77 |
Reflection shell | Resolution: 1.7→1.8 Å / Num. unique obs: 3523 / CC1/2: 0.901 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RDN Resolution: 1.7→38.12 Å / SU ML: 0.1712 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5469 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: 24.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→38.12 Å
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Refine LS restraints |
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LS refinement shell |
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