+Open data
-Basic information
Entry | Database: PDB / ID: 7ogj | ||||||||||||
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Title | Crystal structure of human METTL1 in complex with SAH | ||||||||||||
Components | tRNA (guanine-N(7)-)-methyltransferase | ||||||||||||
Keywords | TRANSFERASE / METTL1 / Complex / SAH | ||||||||||||
Function / homology | Function and homology information internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol / tRNA methylation ...internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol / tRNA methylation / tRNA modification / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / nucleolus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||||||||
Authors | Nai, F. / Bedi, R.K. / Caflisch, A. | ||||||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Acs Bio Med Chem Au / Year: 2023 Title: Small-Molecule Inhibitors of the m7G-RNA Writer METTL1 Authors: Nai, F. / Flores Espinoza, M.P. / Invernizzi, A. / Vargas-Rosales, P.A. / Bobileva, O. / Herok, M. / Caflisch, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ogj.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ogj.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ogj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/7ogj ftp://data.pdbj.org/pub/pdb/validation_reports/og/7ogj | HTTPS FTP |
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-Related structure data
Related structure data | 7pl1C 3ckkS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29178.330 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL1, C12orf1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9UBP6, tRNA (guanine46-N7)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 6 types, 596 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-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: 3.03 Å3/Da / Density % sol: 59.39 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 200 mM lithium sulfate, 20% PEG 1000, 100 mM phosphate-citrate buffer pH 4.2 |
-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: Apr 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→46.92 Å / Num. obs: 96318 / % possible obs: 99.9 % / Redundancy: 8.13 % / Biso Wilson estimate: 24.01 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.34 |
Reflection shell | Resolution: 1.59→1.68 Å / Num. unique obs: 15366 / CC1/2: 0.664 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CKK Resolution: 1.59→46.92 Å / SU ML: 0.2319 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3024 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: 31.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→46.92 Å
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Refine LS restraints |
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LS refinement shell |
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