+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17531 | |||||||||
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Title | SerRS bound to serine tRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | tRNA / SerRS / Serine tRNA / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / mitochondrial seryl-tRNA aminoacylation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / selenocysteine incorporation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis ...selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / mitochondrial seryl-tRNA aminoacylation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / selenocysteine incorporation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis / tRNA binding / molecular adaptor activity / cytoplasmic translation / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / extracellular exosome / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Trichoplusia ni (cabbage looper) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Throll P / Dolce LG / Kowalinski E | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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 | emd_17531.map.gz | 313.7 MB | EMDB map data format | |
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Header (meta data) | emd-17531-v30.xml emd-17531.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17531_fsc.xml | 18.3 KB | Display | FSC data file |
Images | emd_17531.png | 43.5 KB | ||
Masks | emd_17531_msk_1.map | 634.7 MB | Mask map | |
Filedesc metadata | emd-17531.cif.gz | 5.2 KB | ||
Others | emd_17531_half_map_1.map.gz emd_17531_half_map_2.map.gz | 589.6 MB 589.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17531 | HTTPS FTP |
-Validation report
Summary document | emd_17531_validation.pdf.gz | 834.4 KB | Display | EMDB validaton report |
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Full document | emd_17531_full_validation.pdf.gz | 834 KB | Display | |
Data in XML | emd_17531_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | emd_17531_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17531 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17531 | HTTPS FTP |
-Related structure data
Related structure data | 8owxC 8owyC 8p7bC 8p7cC 8p7dC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17531.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_17531_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17531_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17531_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
Entire | Name: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry |
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Components |
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-Supramolecule #1: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
Supramolecule | Name: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Sers
Supramolecule | Name: Sers / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: tRNA
Supramolecule | Name: tRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: SerRS homodimer
Macromolecule | Name: SerRS homodimer / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVLDLDLFRV DKGGDPALIR ETQEKRFKDP GLVDQLVKAD SEWRRCRFRA DNLNKLKNLC SKTIGEKMKK KEPVGDDESV PENVLSFDDL TADALANLKV SQIKKVRLLI DEAILKCDAE RIKLEAERFE NLREIGNLLH PSVPISNDED VDNKVERIWG DCTVRKKYSH ...String: MVLDLDLFRV DKGGDPALIR ETQEKRFKDP GLVDQLVKAD SEWRRCRFRA DNLNKLKNLC SKTIGEKMKK KEPVGDDESV PENVLSFDDL TADALANLKV SQIKKVRLLI DEAILKCDAE RIKLEAERFE NLREIGNLLH PSVPISNDED VDNKVERIWG DCTVRKKYSH VDLVVMVDGF EGEKGAVVAG SRGYFLKGVL VFLEQALIQY ALRTLGSRGY IPIYTPFFMR KEVMQEVAQL SQFDEELYKV IGKGSEKSDD NSYDEKYLIA TSEQPIAALH RDEWLRPEDL PIKYAGLSTC FRQEVGSHGR DTRGIFRVHQ FEKIEQFVYS SPHDNKSWEM FEEMITTAEE FYQSLGIPYH IVNIVSGSLN HAASKKLDLE AWFPGSGAFR ELVSCSNCTD YQARRLRIRY GQTKKMMDKV EFVHMLNATM CATTRTICAI LENYQTEKGI TVPEKLKEFM PPGLQELIPF VKPAPIEQEP SKKQKKQHEG SKKKAAARDV TLENRLQNME VTDA UniProtKB: Serine--tRNA ligase, cytoplasmic |
-Macromolecule #2: Serine tRNA
Macromolecule | Name: Serine tRNA / type: rna / ID: 2 |
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Source (natural) | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GCAGUGGUGG C(4AC)GAGU(OMG)G(H2U)U AAGGC(M2G)UCGG A(JMH)UUGA(6IA)A(PSU)C CGA(OMU)UCGCUC UGCGAG(5MC)GUG GG(5MU)(PSU)CG(1MA)AUC CCACCCACUG CGCCA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-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: FIELD EMISSION GUN |
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 |