+Open data
-Basic information
Entry | Database: PDB / ID: 8d59 | ||||||||||||
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Title | Crystal structure of human METTL1 in complex with SAM | ||||||||||||
Components | tRNA (guanine-N(7)-)-methyltransferase | ||||||||||||
Keywords | TRANSFERASE / Cancer protein | ||||||||||||
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 modification ...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 modification / tRNA methylation / 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: 2.26 Å | ||||||||||||
Authors | Raj, R. / Babu, K. / Nam, Y. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nature / Year: 2023 Title: Structures and mechanisms of tRNA methylation by METTL1-WDR4. Authors: Victor M Ruiz-Arroyo / Rishi Raj / Kesavan Babu / Otgonbileg Onolbaatar / Paul H Roberts / Yunsun Nam / Abstract: Specific, regulated modification of RNAs is important for proper gene expression. tRNAs are rich with various chemical modifications that affect their stability and function. 7-Methylguanosine (mG) ...Specific, regulated modification of RNAs is important for proper gene expression. tRNAs are rich with various chemical modifications that affect their stability and function. 7-Methylguanosine (mG) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth. The METTL1-WDR4 complex generates mG46 in humans, and dysregulation of METTL1-WDR4 has been linked to brain malformation and multiple cancers. Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1-WDR4 and cryo-electron microscopy structures of METTL1-WDR4-tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1-WDR4-tRNA with S-adenosylmethionine or S-adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate mG methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying mG modification by METTL1, providing the framework to understand its contribution to biology and disease. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d59.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d59.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 8d59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d59_validation.pdf.gz | 758.7 KB | Display | wwPDB validaton report |
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Full document | 8d59_full_validation.pdf.gz | 758.6 KB | Display | |
Data in XML | 8d59_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 8d59_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d59 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d59 | HTTPS FTP |
-Related structure data
Related structure data | 8d58C 8d5bC 8d9kC 8d9lC 8eg0C 3ckkS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30412.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL1, C12orf1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: Q9UBP6, tRNA (guanine46-N7)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 6 types, 59 molecules
#2: Chemical | ChemComp-SAM / | ||||||
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#3: Chemical | ChemComp-GOL / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CAC / | #6: Chemical | ChemComp-CL / | #7: 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: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 50 mM Sodium cacodylate pH 5.7, 1.5 M Lithium sulfate, 10 mM Magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→37.25 Å / Num. obs: 12936 / % possible obs: 99.2 % / Redundancy: 15.5 % / Biso Wilson estimate: 47.02 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.07 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.89 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 579 / CC1/2: 0.414 / Rpim(I) all: 0.797 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CKK Resolution: 2.26→37.25 Å / SU ML: 0.2414 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.0713 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.48 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→37.25 Å
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Refine LS restraints |
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LS refinement shell |
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