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- PDB-8p7c: CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry -

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Basic information

Entry
Database: PDB / ID: 8p7c
TitleCryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry
Components
  • Serine tRNA
  • Serine--tRNA ligase, cytoplasmic
  • tRNA N(3)-methylcytidine methyltransferase METTL6
KeywordsRNA BINDING PROTEIN / METTL6 / tRNA / SerRS / Serine tRNA / 3-Methylcytosine
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 / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / 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 / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / 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
S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / Serine--tRNA ligase, cytoplasmic / tRNA N(3)-methylcytidine methyltransferase METTL6
Similarity search - Component
Biological speciesHomo sapiens (human)
Trichoplusia ni (cabbage looper)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsThroll, P. / Dolce, L.G. / Kowalinski, E.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: to be published
Title: Structural basis of the cooperation between the m3C-RNA-methyltransferase METTL6 with SerRS amino-acyl-synthetase for tRNA recognition
Authors: Throll, P. / Dolce, L.G. / Lastres, P.R. / Arnold, K. / Tengo, L. / Basu, S. / Kaiser, S. / Schneider, R. / Kowalinski, E.
History
DepositionMay 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Serine--tRNA ligase, cytoplasmic
D: Serine--tRNA ligase, cytoplasmic
A: tRNA N(3)-methylcytidine methyltransferase METTL6
R: Serine tRNA
C: tRNA N(3)-methylcytidine methyltransferase METTL6
T: Serine tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,47414
Polymers239,5606
Non-polymers9158
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules BDAC

#1: Protein Serine--tRNA ligase, cytoplasmic / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 58863.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARS1, SARS, SERS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49591, serine-tRNA ligase
#2: Protein tRNA N(3)-methylcytidine methyltransferase METTL6 / Methyltransferase-like protein 6 / hMETTL6


Mass: 33296.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL6 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8TCB7, Transferases; Transferring one-carbon groups; Methyltransferases

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RNA chain , 1 types, 2 molecules RT

#3: RNA chain Serine tRNA


Mass: 27620.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper)

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Non-polymers , 3 types, 10 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 63.27 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105928 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02414918
ELECTRON MICROSCOPYf_angle_d1.75521013
ELECTRON MICROSCOPYf_dihedral_angle_d14.2718347
ELECTRON MICROSCOPYf_chiral_restr0.122474
ELECTRON MICROSCOPYf_plane_restr0.0082076

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