+Open data
-Basic information
Entry | Database: PDB / ID: 6we8 | ||||||
---|---|---|---|---|---|---|---|
Title | YTH domain of human YTHDC1 | ||||||
Components | YTH domain-containing protein 1 | ||||||
Keywords | DNA BINDING PROTEIN / N6-methyladenine binding protein domain | ||||||
Function / homology | Function and homology information primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / 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 / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / 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: 1.18 Å | ||||||
Authors | Horton, J.R. / Cheng, X. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Authors: Woodcock, C.B. / Horton, J.R. / Zhou, J. / Bedford, M.T. / Blumenthal, R.M. / Zhang, X. / Cheng, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6we8.cif.gz | 175.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6we8.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 6we8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6we8_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6we8_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 6we8_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6we8_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/6we8 ftp://data.pdbj.org/pub/pdb/validation_reports/we/6we8 | HTTPS FTP |
-Related structure data
Related structure data | 6we9C 6weaC 4r3hS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
|
-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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96MU7 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.22 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1-0.15M ammonium sulfate 0.1 M Bis-Tris pH 5.5 25-29% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→20.01 Å / Num. obs: 93137 / % possible obs: 86.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 11.05 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.038 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.18→1.22 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2859 / CC1/2: 0.41 / CC star: 0.763 / Rpim(I) all: 0.517 / % possible all: 26.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4r3h Resolution: 1.18→20.01 Å / SU ML: 0.0923 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.183 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→20.01 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|