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- EMDB-72370: Trm10-tRNA complex (Two Trm10 monomers bound to one tRNA) -

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Basic information

Entry
Database: EMDB / ID: EMD-72370
TitleTrm10-tRNA complex (Two Trm10 monomers bound to one tRNA)
Map dataFull map
Sample
  • Complex: Ternary complex of two Trm10 molecules bound to tRNA
    • RNA: Transfer RNA (Gly)
    • Protein or peptide: tRNA (guanine(9)-N1)-methyltransferase
  • Ligand: 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
KeywordsSPOUT methyltransferase / tRNA / methylation / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNA (guanine) methyltransferase activity / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA N1-guanine methylation / tRNA modification / tRNA methylation / tRNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
tRNA (guanine(9)-N(1))-methyltransferase TRM10/TRM10A / tRNA (guanine-N1-)-methyltransferase, eukaryotic / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD
Similarity search - Domain/homology
tRNA (guanine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsNandi S / Strassler SE / Conn GL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM130135-07 United States
CitationJournal: bioRxiv / Year: 2025
Title: Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10.
Authors: Suparno Nandi / Sarah E Strassler / Debayan Dey / Aiswarya Krishnamohan / George M Harris / Lindsay R Comstock / Jane E Jackman / Graeme L Conn /
Abstract: The evolutionarily conserved methyltransferase Trm10 modifies the N1 position of guanosine 9 (G9) in some tRNAs, but how the enzyme recognizes and modifies its substrate tRNAs remains unclear. Here, ...The evolutionarily conserved methyltransferase Trm10 modifies the N1 position of guanosine 9 (G9) in some tRNAs, but how the enzyme recognizes and modifies its substrate tRNAs remains unclear. Here, we used an S-adenosyl-L-methionine (SAM) analog to trap the Trm10-tRNA complex and enable determination of its structure in a post-catalytic state by cryogenic electron microscopy (cryo-EM). We observed three distinct complexes: two with a single Trm10 bound to tRNA that differ in their tRNA acceptor stem orientation ("closed" and "open") and a minor population with two Trm10s engaging the same tRNA. The monomeric complexes reveal a positively charged surface that guides the G9 into the catalytic site with key conserved residues forming "pincer"-like interactions that stabilize the flipped methylated nucleotide. In the open tRNA conformation, the acceptor stem is rotated away from the enzyme, weakening the tRNA-protein contacts, consistent with a product-release conformation. The dimeric complex, which is supported by tRNA-dependent protein crosslinking, reveals one Trm10 positioned similarly to the monomeric complexes and engaged with G9, while the other Trm10 contacts distal tRNA regions, suggesting a potential role in facilitating a key conformational transition during the process of catalysis or modified tRNA release. Finally, molecular dynamics simulations comparing G9- and A9-containing complexes reveal that G9 is efficiently stabilized in the binding pocket unlike A9, identifying the structural basis for guanosine selectivity. Overall, these findings reveal the structural determinants of G9-specific tRNA methylation by Trm10 and suggest a unique mechanism of action among RNA-modifying SPOUT methyltransferases.
History
DepositionAug 27, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72370.png

Downloads & links

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Map

FileDownload / File: emd_72370.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.035037354 - 0.09220235
Average (Standard dev.)-0.000033418295 (±0.0022560782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72370_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: CryoSPARC-sharpened map

Fileemd_72370_additional_1.map
AnnotationCryoSPARC-sharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A of the full map

Fileemd_72370_half_map_1.map
AnnotationHalf map A of the full map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the full map

Fileemd_72370_half_map_2.map
AnnotationHalf map B of the full map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Ternary complex of two Trm10 molecules bound to tRNA

EntireName: Ternary complex of two Trm10 molecules bound to tRNA
Components
  • Complex: Ternary complex of two Trm10 molecules bound to tRNA
    • RNA: Transfer RNA (Gly)
    • Protein or peptide: tRNA (guanine(9)-N1)-methyltransferase
  • Ligand: 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine

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Supramolecule #1: Ternary complex of two Trm10 molecules bound to tRNA

SupramoleculeName: Ternary complex of two Trm10 molecules bound to tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Transfer RNA (Gly)

MacromoleculeName: Transfer RNA (Gly) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.83252 KDa
SequenceString:
GCGCAAGAGG UUUAGUGGUA AAAUCCAACG UUGCCAUCGU UGGGCCCCCG GUUCGAUUCC GGGCUUGCGC A

GENBANK: GENBANK: CP023996.1

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Macromolecule #2: tRNA (guanine(9)-N1)-methyltransferase

MacromoleculeName: tRNA (guanine(9)-N1)-methyltransferase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: tRNA (guanine9-N1)-methyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.583582 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNDEINQNE EKVKRTPPLP PVPEGMSKKQ WKKMCKRQRW EENKAKYNAE RRVKKKRLRH ERSAKIQEYI DRGEEVPQEL IREPRINVN QTDSGIEIIL DCSFDELMND KEIVSLSNQV TRAYSANRRA NHFAEIKVAP FDKRLKQRFE TTLKNTNYEN W NHFKFLPD ...String:
MSNDEINQNE EKVKRTPPLP PVPEGMSKKQ WKKMCKRQRW EENKAKYNAE RRVKKKRLRH ERSAKIQEYI DRGEEVPQEL IREPRINVN QTDSGIEIIL DCSFDELMND KEIVSLSNQV TRAYSANRRA NHFAEIKVAP FDKRLKQRFE TTLKNTNYEN W NHFKFLPD DKIMFGDEHI SKDKIVYLTA DTEEKLEKLE PGMRYIVGGI VDKNRYKELC LKKAQKMGIP TRRLPIDEYI NL EGRRVLT TTHVVQLMLK YFDDHNWKNA FESVLPPRKL DAEAKSASSS PAPKDT

UniProtKB: tRNA (guanine(9)-N1)-methyltransferase

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Macromolecule #3: 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine

MacromoleculeName: 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
type: ligand / ID: 3 / Number of copies: 1 / Formula: AN6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 395.414 Da
Chemical component information

ChemComp-AN6:
5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine

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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
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number real images: 26645 / Average exposure time: 2.0 sec. / Average electron dose: 59.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 14103903
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 156897
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: integrative model
Details: chain B of the model is from PDB 4JWJ. Chain A was prepared using AlphaFold.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9xzs:
Trm10-tRNA complex (Two Trm10 monomers bound to one tRNA)

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