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- PDB-7rx8: Structure of METTL3-METTL14(R298H) mutant methyltransferase complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rx8 | ||||||
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Title | Structure of METTL3-METTL14(R298H) mutant methyltransferase complex | ||||||
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![]() | TRANSFERASE / RNA methyltransferase complex / mutant | ||||||
Function / homology | ![]() 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 / RNA methyltransferase activity / mRNA modification / 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 / RNA methyltransferase activity / mRNA modification / 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 / gliogenesis / S-adenosyl-L-methionine binding / mRNA stabilization / regulation of hematopoietic stem cell differentiation / regulation of neuron differentiation / regulation of T cell 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 splicing, via spliceosome / circadian rhythm / mRNA processing / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, P. / Nam, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of METTL3-METTL14(R298H) mutant methyltransferase complex Authors: Zhang, C. / Nam, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.9 KB | Display | ![]() |
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PDB format | ![]() | 182.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5k7mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase |
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#2: Protein | Mass: 39554.652 Da / Num. of mol.: 1 / Mutation: R298H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.84 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.849→50 Å / Num. obs: 52967 / % possible obs: 100 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 1.849→50 Å / Rmerge(I) obs: 1.24 / Num. unique obs: 5223 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5k7m Resolution: 1.85→46.57 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.42 Å2 / Biso mean: 28.3549 Å2 / Biso min: 6.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→46.57 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Origin x: -21.5807 Å / Origin y: 8.4596 Å / Origin z: -12.2584 Å
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Refinement TLS group |
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