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- PDB-7ni8: Crystal structure of the human METTL3-METTL14 complex with compou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ni8 | ||||||
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Title | Crystal structure of the human METTL3-METTL14 complex with compound UOZ040a | ||||||
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![]() | TRANSFERASE / METTL3 / METTL14 / M6A / Inhibitor / Complex | ||||||
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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bedi, R.K. / Huang, D. / Caflisch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Design of Inhibitors of the m6A-RNA Writer Enzyme METTL3 Authors: Bedi, R.K. / Huang, D. / Li, Y. / Caflisch, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.1 KB | Display | ![]() |
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Full document | ![]() | 799 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nhgC ![]() 7nhhC ![]() 7nhiC ![]() 7nhjC ![]() 7nhvC ![]() 7ni7C ![]() 7ni9C ![]() 7niaC ![]() 7nidC ![]() 7oedC ![]() 7oeeC ![]() 7oefC ![]() 7oegC ![]() 7oehC ![]() 7oeiC ![]() 7oejC ![]() 7oekC ![]() 7oelC ![]() 7oemC ![]() 7oqlC ![]() 7oqoC ![]() 7oqpC ![]() 5l6dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28144.080 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 33621.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-UEE / ( |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 400mM Mg acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45 Å / Num. obs: 28073 / % possible obs: 99.8 % / Redundancy: 6.23 % / Biso Wilson estimate: 40.23 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.75 |
Reflection shell | Resolution: 2.2→2.33 Å / Num. unique obs: 4383 / CC1/2: 0.626 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L6D Resolution: 2.2→44.46 Å / SU ML: 0.3199 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4741 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 43.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→44.46 Å
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Refine LS restraints |
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LS refinement shell |
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