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- EMDB-27264: CryoEM structure of human METTL1-WDR4 in complex with Lys-tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-27264
TitleCryoEM structure of human METTL1-WDR4 in complex with Lys-tRNA
Map dataHuman METTL1-WDR4 proteins in complex with Lys tRNA.
Sample
  • Complex: Human METTL1-WDR4 in complex with Lys-tRNA
    • Protein or peptide: tRNA (guanine-N(7)-)-methyltransferase
    • Protein or peptide: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
    • RNA: RNA (65-MER)
KeywordsCancer protein / Methyl transferase / TRANSFERASE
Function / homology
Function and homology information


internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase activator activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol ...internal mRNA (guanine-N7-)-methyltransferase activity / tRNA stabilization / tRNA (m7G46) methyltransferase complex / tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase activator activity / tRNA methyltransferase complex / tRNA modification in the nucleus and cytosol / tRNA methylation / tRNA modification / enzyme activator activity / Transferases; Transferring one-carbon groups; Methyltransferases / chromosome / tRNA binding / DNA damage response / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit / tRNA (guanine-N-7) methyltransferase catalytic subunit Trm8, eukaryote / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 / tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsRuiz-Arroyo VM / Nam Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM122960 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190259 United States
Welch FoundationI-2115-20220331 United States
CitationJournal: Nature / Year: 2023
Title: Structures and mechanisms of tRNA methylation by METTL1-WDR4.
Authors: Victor M Ruiz-Arroyo / Rishi Raj / Kesavan Babu / Otgonbileg Onolbaatar / Paul H Roberts / Yunsun Nam /
Abstract: Specific, regulated modification of RNAs is important for proper gene expression. tRNAs are rich with various chemical modifications that affect their stability and function. 7-Methylguanosine (mG) ...Specific, regulated modification of RNAs is important for proper gene expression. tRNAs are rich with various chemical modifications that affect their stability and function. 7-Methylguanosine (mG) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth. The METTL1-WDR4 complex generates mG46 in humans, and dysregulation of METTL1-WDR4 has been linked to brain malformation and multiple cancers. Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1-WDR4 and cryo-electron microscopy structures of METTL1-WDR4-tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1-WDR4-tRNA with S-adenosylmethionine or S-adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate mG methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying mG modification by METTL1, providing the framework to understand its contribution to biology and disease.
History
DepositionJun 10, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27264.png

Downloads & links

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Map

FileDownload / File: emd_27264.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman METTL1-WDR4 proteins in complex with Lys tRNA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 144 pix.
= 179.28 Å		1.25 Å/pix.
x 144 pix.
= 179.28 Å		1.25 Å/pix.
x 144 pix.
= 179.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.18323438 - 0.5517554
Average (Standard dev.)0.0056589376 (±0.029522095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 179.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27264_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human METTL1-WDR4 proteins in complex with Lys tRNA. Sharpen map.

Fileemd_27264_additional_1.map
AnnotationHuman METTL1-WDR4 proteins in complex with Lys tRNA. Sharpen map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human METTL1-WDR4 proteins in complex with Lys tRNA. Half map.

Fileemd_27264_half_map_1.map
AnnotationHuman METTL1-WDR4 proteins in complex with Lys tRNA. Half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human METTL1-WDR4 proteins in complex with Lys tRNA. Half map.

Fileemd_27264_half_map_2.map
AnnotationHuman METTL1-WDR4 proteins in complex with Lys tRNA. Half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human METTL1-WDR4 in complex with Lys-tRNA

EntireName: Human METTL1-WDR4 in complex with Lys-tRNA
Components
  • Complex: Human METTL1-WDR4 in complex with Lys-tRNA
    • Protein or peptide: tRNA (guanine-N(7)-)-methyltransferase
    • Protein or peptide: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
    • RNA: RNA (65-MER)

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Supramolecule #1: Human METTL1-WDR4 in complex with Lys-tRNA

SupramoleculeName: Human METTL1-WDR4 in complex with Lys-tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 112 KDa

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Macromolecule #1: tRNA (guanine-N(7)-)-methyltransferase

MacromoleculeName: tRNA (guanine-N(7)-)-methyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA (guanine46-N7)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.516012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAETRNVAG AEAPPPQKRY YRQRAHSNPM ADHTLRYPVK PEEMDWSELY PEFFAPLTQN QSHDDPKDKK EKRAQAQVEF ADIGCGYGG LLVELSPLFP DTLILGLEIR VKVSDYVQDR IRALRAAPAG GFQNIACLRS NAMKHLPNFF YKGQLTKMFF L FPDPHFKR ...String:
MAAETRNVAG AEAPPPQKRY YRQRAHSNPM ADHTLRYPVK PEEMDWSELY PEFFAPLTQN QSHDDPKDKK EKRAQAQVEF ADIGCGYGG LLVELSPLFP DTLILGLEIR VKVSDYVQDR IRALRAAPAG GFQNIACLRS NAMKHLPNFF YKGQLTKMFF L FPDPHFKR TKHKWRIISP TLLAEYAYVL RVGGLVYTIT DVLELHDWMC THFEEHPLFE RVPLEDLSED PVVGHLGTST EE GKKVLRN GGKNFPAIFR RIQDPVLQAV TSQTSLPGH

UniProtKB: tRNA (guanine-N(7)-)-methyltransferase

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Macromolecule #2: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4

MacromoleculeName: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.123023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGSGMAGS VGLALCGQTL VVRGGSRFLA TSIASSDDDS LFIYDCSAAE KKSQENKGED APLDQGSGAI LASTFSKSG SYFALTDDSK RLILFRTKPW QCLSVRTVAR RCTALTFIAS EEKVLVADKS GDVYSFSVLE PHGCGRLELG H LSMLLDVA ...String:
MHHHHHHENL YFQGSGMAGS VGLALCGQTL VVRGGSRFLA TSIASSDDDS LFIYDCSAAE KKSQENKGED APLDQGSGAI LASTFSKSG SYFALTDDSK RLILFRTKPW QCLSVRTVAR RCTALTFIAS EEKVLVADKS GDVYSFSVLE PHGCGRLELG H LSMLLDVA VSPDDRFILT ADRDEKIRVS WAAAPHSIES FCLGHTEFVS RISVVPTQPG LLLSSSGDGT LRLWEYRSGR QL HCCHLAS LQELVDPQAP QKFAASRIAF WCQENCVALL CDGTPVVYIF QLDARRQQLV YRQQLAFQHQ VWDVAFEETQ GLW VLQDCQ EAPLVLYRPV GDQWQSVPES TVLKKVSGVL RGNWAMLEGS AGADASFSSL YKATFDNVTS YLKKKEERLQ QQLE KKQRR

UniProtKB: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4

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Macromolecule #3: RNA (65-MER)

MacromoleculeName: RNA (65-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.162705 KDa
SequenceString:
GCCCGGAUAG CUCAGUCGGU AGAGCAUCAG ACUUUUAAUC UGAGGGUCCA GGGUUCAAGU CCCUGUUCGG GC

GENBANK: GENBANK: MN296912.1

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 273.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 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: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37033
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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