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- PDB-7acd: 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: 7acd | |||||||||
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Title | Crystal structure of the human METTL3-METTL14 complex with compound T30 (UZH1a) | |||||||||
![]() | (N6-adenosine-methyltransferase ...) x 2 | |||||||||
![]() | TRANSFERASE / Inhibitor / Complex / METTL3 / Sinefungin / METTL14 | |||||||||
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: METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes. Authors: Moroz-Omori, E.V. / Huang, D. / Kumar Bedi, R. / Cheriyamkunnel, S.J. / Bochenkova, E. / Dolbois, A. / Rzeczkowski, M.D. / Li, Y. / Wiedmer, L. / Caflisch, A. #1: ![]() Title: METTL3 inhibitors for epitranscriptomic modulation of cellular processes Authors: Moroz-Omori, E.V. / Huang, D. / Bedi, R.K. / Cheriyamkunnel, S.J. / Bochenkova, E. / Dolbois, A. / Rzeczkowski, M.D. / Wiedmer, L. / Caflisch, A. #2: ![]() Title: Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. Authors: Li, Y. / Bedi, R.K. / Moroz-Omori, E.V. / 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 | ![]() | 79.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 760.4 KB | Display | ![]() |
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Full document | ![]() | 767.4 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l6dS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-N6-adenosine-methyltransferase ... , 2 types, 2 molecules AB
#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.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 126 molecules ![](data/chem/img/R72.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-R72 / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-ACT / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.51 % |
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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: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.98 Å / Num. obs: 19248 / % possible obs: 99.9 % / Redundancy: 9.72 % / Biso Wilson estimate: 44.05 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.33 |
Reflection shell | Resolution: 2.5→2.65 Å / Num. unique obs: 3051 / CC1/2: 0.609 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L6D Resolution: 2.5→44.48 Å / SU ML: 0.312 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9113 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: 44.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→44.48 Å
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Refine LS restraints |
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LS refinement shell |
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