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- EMDB-17532: Serine tRNA from Trichoplusia ni -

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Basic information

Entry
Database: EMDB / ID: EMD-17532
TitleSerine tRNA from Trichoplusia ni
Map data
Sample
  • Complex: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
    • RNA: Serine tRNA
KeywordsSerine tRNA / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human) / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsThroll P / Dolce LG / Kowalinski E
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: 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
DepositionMay 30, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17532.png

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Map

FileDownload / File: emd_17532.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 258. Å		0.65 Å/pix.
x 400 pix.
= 258. Å		0.65 Å/pix.
x 400 pix.
= 258. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.152
Minimum - Maximum-0.0825989 - 0.6041469
Average (Standard dev.)-0.00041419806 (±0.0155672375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17532_msk_1.map
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Half map: #1

Fileemd_17532_half_map_1.map
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Half map: #2

Fileemd_17532_half_map_2.map
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Sample components

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Entire : METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry

EntireName: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
Components
  • Complex: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
    • RNA: Serine tRNA

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Supramolecule #1: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry

SupramoleculeName: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine tRNA

MacromoleculeName: Serine tRNA / type: rna / ID: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
SequenceString:
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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 63.27 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112675
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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