+Open data
-Basic information
Entry | Database: PDB / ID: 7z4u | ||||||
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Title | Crystal structure of YTHDF2 with compound YLI_DF_028 | ||||||
Components | YTH domain-containing family protein 2 | ||||||
Keywords | RNA BINDING PROTEIN / epitranscriptomic reader / m6A reader | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Nai, F. / Li, Y. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z4u.cif.gz | 93.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z4u.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 7z4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z4u_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7z4u_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7z4u_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7z4u_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/7z4u ftp://data.pdbj.org/pub/pdb/validation_reports/z4/7z4u | HTTPS FTP |
-Related structure data
Related structure data | 7r5fC 7r5lC 7r5wC 7ywbC 7yx6C 7yxeC 7z26C 7z54C 7z5mC 7z7bC 7z7fC 7z8pC 7z8wC 7z8xC 7z92C 7z93C 7zg4C 4rdnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: YTHDF2, HGRG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5A9 |
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-Non-polymers , 5 types, 132 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 2 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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→44.06 Å / Num. obs: 72603 / % possible obs: 99.8 % / Redundancy: 6.35 % / Biso Wilson estimate: 30.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.49 |
Reflection shell | Resolution: 1.83→1.94 Å / Num. unique obs: 11597 / CC1/2: 0.703 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RDN Resolution: 1.83→44.06 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 27.2861 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: 34.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→44.06 Å
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Refine LS restraints |
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LS refinement shell |
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