[English] 日本語
Yorodumi- PDB-7rx7: Structure of METTL3-METTL14(R298P) mutant methyltransferase complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rx7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of METTL3-METTL14(R298P) mutant methyltransferase complex | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / RNA methyltransferase complex / mutant | ||||||
Function / homology | Function and homology information negative regulation of hematopoietic progenitor cell differentiation / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / adenosine to inosine editing / RNA methyltransferase activity / endothelial to hematopoietic transition / RNA methylation ...negative regulation of hematopoietic progenitor cell differentiation / mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / adenosine to inosine editing / RNA methyltransferase activity / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / primary miRNA processing / dosage compensation by inactivation of X chromosome / : / forebrain radial glial cell differentiation / S-adenosyl-L-methionine binding / gliogenesis / mRNA stabilization / regulation of hematopoietic stem cell differentiation / regulation of T cell differentiation / regulation of neuron differentiation / negative regulation of type I interferon-mediated signaling pathway / stem cell population maintenance / oogenesis / mRNA destabilization / negative regulation of Notch signaling pathway / mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of translation / mRNA processing / mRNA splicing, via spliceosome / circadian rhythm / cellular response to UV / spermatogenesis / nuclear body / nuclear speck / protein heterodimerization activity / innate immune response / mRNA binding / DNA damage response / Golgi apparatus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.645 Å | ||||||
Authors | Wang, P. / Nam, Y. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Structure of METTL3-METTL14(R298P) mutant methyltransferase complex Authors: Zhang, C. / Nam, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rx7.cif.gz | 236.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rx7.ent.gz | 186.1 KB | Display | PDB format |
PDBx/mmJSON format | 7rx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rx7_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7rx7_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 7rx7_validation.xml.gz | 24 KB | Display | |
Data in CIF | 7rx7_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/7rx7 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/7rx7 | HTTPS FTP |
-Related structure data
Related structure data | 5k7mS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25732.504 Da / Num. of mol.: 1 / Fragment: Catalytic domain residues 357-580 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3, MTA70 / Production host: Escherichia coli (E. coli) References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase |
---|---|
#2: Protein | Mass: 39513.621 Da / Num. of mol.: 1 / Mutation: R298P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14, KIAA1627 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HCE5 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.97 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris (pH 8.0) and 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97938 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97938 Å / Relative weight: 1 |
Reflection | Resolution: 1.645→50 Å / Num. obs: 74404 / % possible obs: 99.6 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.645→1.71 Å / Rmerge(I) obs: 0.892 / Num. unique obs: 7285 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5k7m Resolution: 1.645→46.564 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.57 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.47 Å2 / Biso mean: 24.6641 Å2 / Biso min: 3.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.645→46.564 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -21.4395 Å / Origin y: 8.8101 Å / Origin z: -12.0696 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|