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Yorodumi- PDB-8pwa: Crystal structure of the human METTL3-METTL14 in complex with a b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pwa | ||||||
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Title | Crystal structure of the human METTL3-METTL14 in complex with a bisubstrate analogue (BA4) | ||||||
Components | (N6-adenosine-methyltransferase ...) x 2 | ||||||
Keywords | TRANSFERASE / METTL3 / bisubstrate / complex / m6A | ||||||
Function / homology | Function and homology information mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / RNA N6-methyladenosine methyltransferase complex / mRNA m(6)A methyltransferase activity / positive regulation of cap-independent translational initiation / adenosine to inosine editing / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / RNA methylation ...mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity / mRNA m6A methyltransferase / RNA N6-methyladenosine methyltransferase complex / mRNA m(6)A methyltransferase activity / positive regulation of cap-independent translational initiation / adenosine to inosine editing / endothelial to hematopoietic transition / RNA methyltransferase activity / regulation of meiotic cell cycle / RNA methylation / primary miRNA processing / : / forebrain radial glial cell differentiation / dosage compensation by inactivation of X chromosome / S-adenosyl-L-methionine binding / gliogenesis / regulation of hematopoietic stem cell differentiation / regulation of T cell differentiation / negative regulation of type I interferon-mediated signaling pathway / oogenesis / stem cell population maintenance / 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: 2.1 Å | ||||||
Authors | Bedi, R.K. / Etheve-Quelquejeu, M. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Elife / Year: 2024 Title: The catalytic mechanism of the RNA methyltransferase METTL3. Authors: Corbeski, I. / Vargas-Rosales, P.A. / Bedi, R.K. / Deng, J. / Coelho, D. / Braud, E. / Iannazzo, L. / Li, Y. / Huang, D. / Etheve-Quelquejeu, M. / Cui, Q. / Caflisch, A. #1: Journal: Elife / Year: 2023 Title: The catalytic mechanism of the RNA methyltransferase METTL3 Authors: Corbeski, I. / Vargas-Rosales, P.A. / Bedi, R.K. / Deng, J. / Coelho, D. / Braud, E. / Iannazzo, L. / Li, Y. / Huang, D. / Etheve-Quelquejeu, M. / Cui, Q. / Caflisch, A. #2: Journal: Biorxiv / Year: 2023 Title: The catalytic mechanism of the RNA methyltransferase METTL3. Authors: Corbeski, I. / Vargas-Rosales, P.A. / Bedi, R.K. / Deng, J. / Coelho, D. / Braud, E. / Iannazzo, L. / Li, Y. / Huang, D. / Etheve-Quelquejeu, M. / Cui, Q. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pwa.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pwa.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 8pwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/8pwa ftp://data.pdbj.org/pub/pdb/validation_reports/pw/8pwa | HTTPS FTP |
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-Related structure data
Related structure data | 8pw8C 8pw9C 8pwbC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-N6-adenosine-methyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 26017.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3, MTA70 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86U44, mRNA m6A methyltransferase |
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#2: Protein | Mass: 33547.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4IFD8 |
-Non-polymers , 4 types, 221 molecules
#3: Chemical | ChemComp-I0C / ( |
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#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.4M Magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45 Å / Num. obs: 32244 / % possible obs: 99.9 % / Redundancy: 9.66 % / Biso Wilson estimate: 38.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.25 |
Reflection shell | Resolution: 2.1→2.23 Å / Num. unique obs: 5091 / CC1/2: 0.682 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.54 Å / SU ML: 0.2423 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9163 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: 43.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.54 Å
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Refine LS restraints |
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LS refinement shell |
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