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Yorodumi- PDB-8q4u: Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q4u | ||||||
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Title | Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b) | ||||||
Components | YTH domain-containing protein 1 | ||||||
Keywords | RNA BINDING PROTEIN / YTHDC1 / inhibitor / complex / reader | ||||||
Function / homology | Function and homology information primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / 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 / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Bedi, R.K. / Zalesak, F. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b) Authors: Bedi, R.K. / Zalesak, F. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q4u.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q4u.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 8q4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/8q4u ftp://data.pdbj.org/pub/pdb/validation_reports/q4/8q4u | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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
#1: Protein | Mass: 18823.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | 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: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.2M Ammonium Sulphate, 0.1M Bis-Tris pH 6.5 |
-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: Apr 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→38.7 Å / Num. obs: 68786 / % possible obs: 98.4 % / Redundancy: 3.37 % / Biso Wilson estimate: 24.13 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.37→1.45 Å / Num. unique obs: 10882 / CC1/2: 0.647 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→38.7 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6443 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: 32.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→38.7 Å
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Refine LS restraints |
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LS refinement shell |
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