+Open data
-Basic information
Entry | Database: PDB / ID: 9h35 | ||||||
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Title | Crystal structure of the YTHDC2 YTH domain | ||||||
Components | 3'-5' RNA helicase YTHDC2 | ||||||
Keywords | RNA BINDING PROTEIN / YTHDC1 / inhibitor / complex / reader | ||||||
Function / homology | Function and homology information germline cell cycle switching, mitotic to meiotic cell cycle / ribonucleoprotein granule / positive regulation by host of viral genome replication / 3'-5' RNA helicase activity / N6-methyladenosine-containing RNA reader activity / oocyte development / ATP-dependent activity, acting on RNA / RNA polymerase binding / spermatid development / response to tumor necrosis factor ...germline cell cycle switching, mitotic to meiotic cell cycle / ribonucleoprotein granule / positive regulation by host of viral genome replication / 3'-5' RNA helicase activity / N6-methyladenosine-containing RNA reader activity / oocyte development / ATP-dependent activity, acting on RNA / RNA polymerase binding / spermatid development / response to tumor necrosis factor / response to interleukin-1 / meiotic cell cycle / helicase activity / RNA helicase / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Bedi, R.K. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the YTHDC2 YTH domain Authors: Bedi, R.K. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9h35.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9h35.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 9h35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9h35_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 9h35_full_validation.pdf.gz | 454.2 KB | Display | |
Data in XML | 9h35_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 9h35_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/9h35 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/9h35 | HTTPS FTP |
-Related structure data
Related structure data | 9h36C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16270.419 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6S0, RNA helicase #2: Water | ChemComp-HOH / | Has protein modification | N | |
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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: 3.07 Å3/Da / Density % sol: 59.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 50 mM ammonium sulfate, 5 mM BIS-TRIS pH 6.5, 30 % PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 27, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→48.8 Å / Num. obs: 43492 / % possible obs: 100 % / Redundancy: 10.71 % / Biso Wilson estimate: 77.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 2.68→2.86 Å / Num. unique obs: 7664 / CC1/2: 0.585 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→48.79 Å / SU ML: 0.5319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1791 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: 74.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→48.79 Å
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Refine LS restraints |
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LS refinement shell |
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