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Open data
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Basic information
Entry | Database: PDB / ID: 7yxe | ||||||
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Title | Crystal structure of YTHDF2 with compound ZA_143 | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Nai, F. / Zalesak, 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 | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 57.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r5fC ![]() 7r5lC ![]() 7r5wC ![]() 7ywbC ![]() 7yx6C ![]() 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 | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19367.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 155 molecules ![](data/chem/img/I82.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 2.05 M Ammonium sulfate, 0.1 M Sodium citrate tribasic pH 5.1 |
-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: Dec 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→44.06 Å / Num. obs: 35681 / % possible obs: 99.9 % / Redundancy: 10.18 % / Biso Wilson estimate: 27.98 Å2 / CC1/2: 1 / Net I/σ(I): 34.13 |
Reflection shell | Resolution: 1.85→1.96 Å / Num. unique obs: 5741 / CC1/2: 0.936 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RDN Resolution: 1.85→44.06 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6627 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: 30.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→44.06 Å
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Refine LS restraints |
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LS refinement shell |
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