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- EMDB-17529: CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry -
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Open data
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Basic information
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Title | CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry | |||||||||
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![]() | METTL6 / tRNA / SerRS / Serine tRNA / 3-Methylcytosine / RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() selenocysteine-tRNA ligase activity / tRNA (cytidine-3-)-methyltransferase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / Cytosolic tRNA aminoacylation / tRNA modification / tRNA methylation ...selenocysteine-tRNA ligase activity / tRNA (cytidine-3-)-methyltransferase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / Cytosolic tRNA aminoacylation / tRNA modification / tRNA methylation / Selenocysteine synthesis / negative regulation of angiogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasmic translation / tRNA binding / molecular adaptor activity / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Throll P / Dolce LG / Kowalinski E | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural basis of tRNA recognition by the mC RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase. Authors: Philipp Throll / Luciano G Dolce / Palma Rico-Lastres / Katharina Arnold / Laura Tengo / Shibom Basu / Stefanie Kaiser / Robert Schneider / Eva Kowalinski / ![]() ![]() Abstract: Methylation of cytosine 32 in the anticodon loop of tRNAs to 3-methylcytosine (mC) is crucial for cellular translation fidelity. Misregulation of the RNA methyltransferases setting this modification ...Methylation of cytosine 32 in the anticodon loop of tRNAs to 3-methylcytosine (mC) is crucial for cellular translation fidelity. Misregulation of the RNA methyltransferases setting this modification can cause aggressive cancers and metabolic disturbances. Here, we report the cryo-electron microscopy structure of the human mC tRNA methyltransferase METTL6 in complex with seryl-tRNA synthetase (SerRS) and their common substrate tRNA. Through the complex structure, we identify the tRNA-binding domain of METTL6. We show that SerRS acts as the tRNA substrate selection factor for METTL6. We demonstrate that SerRS augments the methylation activity of METTL6 and that direct contacts between METTL6 and SerRS are necessary for efficient tRNA methylation. Finally, on the basis of the structure of METTL6 in complex with SerRS and tRNA, we postulate a universal tRNA-binding mode for mC RNA methyltransferases, including METTL2 and METTL8, suggesting that these mammalian paralogs use similar ways to engage their respective tRNA substrates and cofactors. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 311.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.8 KB 16.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.3 KB | Display | ![]() |
Images | ![]() | 19.8 KB | ||
Masks | ![]() | 634.7 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 589.5 MB 589.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p7cMC ![]() 8owxC ![]() 8owyC ![]() 8p7bC ![]() 8p7dC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.645 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry
Entire | Name: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry |
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Components |
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-Supramolecule #1: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry
Supramolecule | Name: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Serine--tRNA ligase, cytoplasmic
Macromolecule | Name: Serine--tRNA ligase, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: serine-tRNA ligase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.863211 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MVLDLDLFRV DKGGDPALIR ETQEKRFKDP GLVDQLVKAD SEWRRCRFRA DNLNKLKNLC SKTIGEKMKK KEPVGDDESV PENVLSFDD LTADALANLK VSQIKKVRLL IDEAILKCDA ERIKLEAERF ENLREIGNLL HPSVPISNDE DVDNKVERIW G DCTVRKKY ...String: MVLDLDLFRV DKGGDPALIR ETQEKRFKDP GLVDQLVKAD SEWRRCRFRA DNLNKLKNLC SKTIGEKMKK KEPVGDDESV PENVLSFDD LTADALANLK VSQIKKVRLL IDEAILKCDA ERIKLEAERF ENLREIGNLL HPSVPISNDE DVDNKVERIW G DCTVRKKY SHVDLVVMVD GFEGEKGAVV AGSRGYFLKG VLVFLEQALI QYALRTLGSR GYIPIYTPFF MRKEVMQEVA QL SQFDEEL YKVIGKGSEK SDDNSYDEKY LIATSEQPIA ALHRDEWLRP EDLPIKYAGL STCFRQEVGS HGRDTRGIFR VHQ FEKIEQ FVYSSPHDNK SWEMFEEMIT TAEEFYQSLG IPYHIVNIVS GSLNHAASKK LDLEAWFPGS GAFRELVSCS NCTD YQARR LRIRYGQTKK MMDKVEFVHM LNATMCATTR TICAILENYQ TEKGITVPEK LKEFMPPGLQ ELIPFVKPAP IEQEP SKKQ KKQHEGSKKK AAARDVTLEN RLQNMEVTDA UniProtKB: Serine--tRNA ligase, cytoplasmic |
-Macromolecule #2: tRNA N(3)-methylcytidine methyltransferase METTL6
Macromolecule | Name: tRNA N(3)-methylcytidine methyltransferase METTL6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO EC number: Transferases; Transferring one-carbon groups; Methyltransferases |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.296055 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MASLQRKGLQ ARILTSEEEE KLKRDQTLVS DFKQQKLEQE AQKNWDLFYK RNSTNFFKDR HWTTREFEEL RSCREFEDQK LTMLEAGCG VGNCLFPLLE EDPNIFAYAC DFSPRAIEYV KQNPLYDTER CKVFQCDLTK DDLLDHVPPE SVDVVMLIFV L SAVHPDKM ...String: MASLQRKGLQ ARILTSEEEE KLKRDQTLVS DFKQQKLEQE AQKNWDLFYK RNSTNFFKDR HWTTREFEEL RSCREFEDQK LTMLEAGCG VGNCLFPLLE EDPNIFAYAC DFSPRAIEYV KQNPLYDTER CKVFQCDLTK DDLLDHVPPE SVDVVMLIFV L SAVHPDKM HLVLQNIYKV LKPGKSVLFR DYGLYDHAML RFKASSKLGE NFYVRQDGTR SYFFTDDFLA QLFMDTGYEE VV NEYVFRE TVNKKEGLCV PRVFLQSKFL KPPKNPSPVV LGLDPKS UniProtKB: tRNA N(3)-methylcytidine methyltransferase METTL6 |
-Macromolecule #3: Serine tRNA
Macromolecule | Name: Serine tRNA / type: rna / ID: 3 / Number of copies: 2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.620635 KDa |
Sequence | String: GCAGUGGUGG C(4AC)GAGU(OMG)G(H2U)U AAGGC(M2G)UCGG A(JMH)UUGA(6IA)A(PSU)C CGA(OMU)UCGC U CUGCGAG(5MC)GU GGG(5MU)(PSU)CG(1MA)AU CCCACCCACU GCGCCA |
-Macromolecule #4: S-ADENOSYL-L-HOMOCYSTEINE
Macromolecule | Name: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: SAH |
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Molecular weight | Theoretical: 384.411 Da |
Chemical component information | ![]() ChemComp-SAH: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 63.27 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |