[English] 日本語
Yorodumi
- EMDB-17529: CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17529
TitleCryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry
Map data
Sample
  • Complex: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry
    • Protein or peptide: Serine--tRNA ligase, cytoplasmic
    • Protein or peptide: tRNA N(3)-methylcytidine methyltransferase METTL6
    • 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 modification / tRNA methylation ...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 modification / tRNA methylation / Selenocysteine synthesis / Transferases; Transferring one-carbon groups; Methyltransferases / 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
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)-cytidine methyltransferase METTL6
Similarity search - Component
Biological speciesHomo sapiens (human) / Trichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17529.png

Downloads & links

-
Map

FileDownload / File: emd_17529.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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-0.1676051 - 0.61092323
Average (Standard dev.)0.0007087822 (±0.018042801)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_17529_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17529_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_17529_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

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

EntireName: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry
Components
  • Complex: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry
    • Protein or peptide: Serine--tRNA ligase, cytoplasmic
    • Protein or peptide: tRNA N(3)-methylcytidine methyltransferase METTL6
    • RNA: Serine tRNA
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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

SupramoleculeName: METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
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

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

MacromoleculeName: tRNA N(3)-methylcytidine methyltransferase METTL6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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)-cytidine methyltransferase METTL6

-
Macromolecule #3: Serine tRNA

MacromoleculeName: Serine tRNA / type: rna / ID: 3 / Number of copies: 2
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

-
Macromolecule #4: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4rqe

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105928
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more