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Yorodumi- PDB-6ttt: Crystal structure of the human METTL3-METTL14 complex bound to Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ttt | ||||||
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Title | Crystal structure of the human METTL3-METTL14 complex bound to Compound 2 (ASI_M3M_140) | ||||||
Components |
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Keywords | TRANSFERASE / Compound / Complex / Mettl3 / Mettl14 / Epitranscriptomic | ||||||
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 / RNA methyltransferase activity / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle ...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 / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / mRNA modification / primary miRNA processing / dosage compensation by inactivation of X chromosome / forebrain radial glial cell differentiation / S-adenosyl-L-methionine binding / regulation of hematopoietic stem cell differentiation / gliogenesis / mRNA stabilization / regulation of neuron differentiation / regulation of T cell differentiation / stem cell population maintenance / negative regulation of type I interferon-mediated signaling pathway / oogenesis / negative regulation of Notch signaling pathway / mRNA destabilization / mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of translation / mRNA splicing, via spliceosome / mRNA processing / 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: 2.3 Å | ||||||
Authors | Bedi, R.K. / Huang, D. / Sledz, P. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Chemmedchem / Year: 2020 Title: Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer. Authors: Bedi, R.K. / Huang, D. / Eberle, S.A. / Wiedmer, L. / Sledz, P. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ttt.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ttt.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ttt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ttt_validation.pdf.gz | 767.2 KB | Display | wwPDB validaton report |
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Full document | 6ttt_full_validation.pdf.gz | 771.6 KB | Display | |
Data in XML | 6ttt_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 6ttt_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/6ttt ftp://data.pdbj.org/pub/pdb/validation_reports/tt/6ttt | HTTPS FTP |
-Related structure data
Related structure data | 6ttpC 6ttvC 6ttwC 6ttxC 6tu1C 6y4gC 5l6dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64562.879 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: 52229.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14, KIAA1627 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HCE5 |
#3: Chemical | ChemComp-NWQ / ( |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350, 200 mM Magnesium acetate |
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-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: Aug 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.8 Å / Num. obs: 24646 / % possible obs: 99.1 % / Redundancy: 6.55 % / Biso Wilson estimate: 46.47 Å2 / CC1/2: 0.991 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.3→2.44 Å / Num. unique obs: 3894 / CC1/2: 0.688 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L6D Resolution: 2.3→49.78 Å / SU ML: 0.2905 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1779
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.78 Å
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Refine LS restraints |
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LS refinement shell |
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