+Open data
-Basic information
Entry | Database: PDB / ID: 7z7f | ||||||
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Title | Crystal structure of YTHDF2 with compound YLI_DC1_005 | ||||||
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 / negative regulation of type I interferon-mediated signaling pathway / hematopoietic stem cell proliferation / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / humoral immune response / regulation of neurogenesis / centriolar satellite / regulation of cell adhesion / stress granule assembly / regulation of mRNA stability / P-body / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / innate immune response / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Nai, F. / Li, Y. / Dolbois, A. / 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 | 7z7f.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z7f.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 7z7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z7f_validation.pdf.gz | 809.6 KB | Display | wwPDB validaton report |
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Full document | 7z7f_full_validation.pdf.gz | 810.5 KB | Display | |
Data in XML | 7z7f_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7z7f_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/7z7f ftp://data.pdbj.org/pub/pdb/validation_reports/z7/7z7f | HTTPS FTP |
-Related structure data
Related structure data | 7r5fC 7r5lC 7r5wC 7ywbC 7yx6C 7yxeC 7z26C 7z4uC 7z54C 7z5mC 7z7bC 7z8pC 7z8wC 7z8xC 7z92C 7z93C 7zg4C 4rdnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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, 153 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-IF3 / ~{ | #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: 2.73 Å3/Da / Density % sol: 55.02 % |
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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 5.0 |
-Data collection
Diffraction | Mean temperature: 277.15 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: Jun 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→44.07 Å / Num. obs: 30570 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 29.99 Å2 / CC1/2: 1 / Net I/σ(I): 41.33 |
Reflection shell | Resolution: 1.94→2.06 Å / Num. unique obs: 4913 / CC1/2: 0.979 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RDN Resolution: 1.95→44.07 Å / SU ML: 0.2241 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.0026 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: 33.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→44.07 Å
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Refine LS restraints |
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LS refinement shell |
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