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- EMDB-17531: SerRS bound to serine tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-17531
TitleSerRS bound to serine tRNA
Map data
Sample
  • Complex: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
    • Complex: Sers
      • Protein or peptide: SerRS homodimer
    • Complex: tRNA
      • RNA: Serine tRNA
KeywordstRNA / SerRS / Serine tRNA / RNA BINDING PROTEIN
Function / homology
Function and homology information


selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis ...selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis / molecular adaptor activity / cytoplasmic translation / tRNA binding / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
Serine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human) / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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_17531.png

Downloads & links

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Map

FileDownload / File: emd_17531.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 550 pix.
= 354.75 Å		0.65 Å/pix.
x 550 pix.
= 354.75 Å		0.65 Å/pix.
x 550 pix.
= 354.75 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: 0.144
Minimum - Maximum-0.1996958 - 0.70298463
Average (Standard dev.)-0.000068159134 (±0.013272917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 354.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17531_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_17531_half_map_1.map
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Half map: #2

Fileemd_17531_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
    • Complex: Sers
      • Protein or peptide: SerRS homodimer
    • Complex: tRNA
      • 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

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Supramolecule #2: Sers

SupramoleculeName: Sers / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: tRNA

SupramoleculeName: tRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: SerRS homodimer

MacromoleculeName: SerRS homodimer / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #2: Serine tRNA

MacromoleculeName: Serine tRNA / type: rna / ID: 2
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: PDB ENTRY
PDB model - PDB ID:

4rqe

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49372
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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