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- EMDB-17528: CryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry -

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Basic information

Entry
Database: EMDB / ID: EMD-17528
TitleCryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
Map data
Sample
  • Complex: METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry
    • Protein or peptide: Serine--tRNA ligase, cytoplasmic
    • Protein or peptide: tRNA N(3)-methylcytidine methyltransferase METTL6
    • RNA: Serine tRNA
    • RNA: Serine tRNA
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsMETTL6 / tRNA / SerRS / Serine tRNA / 3-Methylcytosine / RNA BINDING PROTEIN
Function / homology
Function and homology information


selenocysteine-tRNA ligase activity / tRNA (cytidine-3-)-methyltransferase 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 methylation / tRNA modification ...selenocysteine-tRNA ligase activity / tRNA (cytidine-3-)-methyltransferase 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 methylation / tRNA modification / 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
tRNA N(3)-methylcytidine methyltransferase METTL2/6/8-like / 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 / Methyltransferase type 12 / Methyltransferase domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) ...tRNA N(3)-methylcytidine methyltransferase METTL2/6/8-like / 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 / Methyltransferase type 12 / Methyltransferase domain / 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) / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Serine--tRNA ligase, cytoplasmic / tRNA N(3)-methylcytidine methyltransferase METTL6
Similarity search - Component
Biological speciesHomo sapiens (human) / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 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_17528.png

Downloads & links

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Map

FileDownload / File: emd_17528.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.549822 - 1.5312741
Average (Standard dev.)-0.0006351989 (±0.025856724)
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_17528_msk_1.map
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Half map: #2

Fileemd_17528_half_map_1.map
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Half map: #1

Fileemd_17528_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
    • Protein or peptide: Serine--tRNA ligase, cytoplasmic
    • Protein or peptide: tRNA N(3)-methylcytidine methyltransferase METTL6
    • RNA: Serine tRNA
    • RNA: Serine tRNA
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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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: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine--tRNA ligase, cytoplasmic

MacromoleculeName: Serine--tRNA ligase, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: serine-tRNA ligase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.863211 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #2: tRNA N(3)-methylcytidine methyltransferase METTL6

MacromoleculeName: tRNA N(3)-methylcytidine methyltransferase METTL6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.296055 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #3: Serine tRNA

MacromoleculeName: Serine tRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 27.536477 KDa
SequenceString:
GCAGUGGUGG C(4AC)GAGU(OMG)G(H2U)U AAGGC(M2G)UCGG ACUUGAAA(PSU)C CGA(OMU)UCGCUC UGCGAG (5MC)GU GGG(5MU)(PSU)CG(1MA)AU CCCACCCACU GCGCCA

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Macromolecule #4: Serine tRNA

MacromoleculeName: Serine tRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 27.620635 KDa
SequenceString:
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

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Macromolecule #5: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 460853
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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