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- PDB-9xzr: Trm10-tRNA complex (open conformation) -

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Basic information

Entry
Database: PDB / ID: 9xzr
TitleTrm10-tRNA complex (open conformation)
Components
  • Transfer RNA (Gly)
  • tRNA (guanine(9)-N1)-methyltransferase
KeywordsRNA BINDING PROTEIN/RNA / SPOUT 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
Chem-AN6 / : / RNA / RNA (> 10) / tRNA (guanine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BMN1-35 (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsNandi, S. / Strassler, S.E. / Conn, G.L.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transfer RNA (Gly)
B: tRNA (guanine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7883
Polymers57,3932
Non-polymers3951
Water00
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

#1: RNA chain Transfer RNA (Gly)


Mass: 22809.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1497470354
#2: Protein tRNA (guanine(9)-N1)-methyltransferase / tRNA methyltransferase 10 / tRNA(m1G9)-methyltransferase / tRNA(m1G9)MTase


Mass: 34583.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae BMN1-35 (yeast)
Gene: TRM10, YOL093W, O0926 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q12400, tRNA (guanine9-N1)-methyltransferase
#3: Chemical ChemComp-AN6 / 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine


Type: L-peptide linking / Mass: 395.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N7O5 / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
Has ligand of interestN
Has protein modificationN

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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: Trm10-tRNA complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 2 sec. / Electron dose: 59.82 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 26645
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2Leginonimage acquisition
4cryoSPARC4.5.3CTF correction
7UCSF Chimera1.17.3model fitting
9cryoSPARC4.5.3initial Euler assignment
10cryoSPARC4.5.3final Euler assignment
11cryoSPARC4.5.3classification
12cryoSPARC4.5.33D reconstruction
13PHENIX1.21.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 14103903
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1440392 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: chain B of the model is from PDB 4JWJ. Chain A was prepared using AlphaFold.
Source name: Other / Type: integrative model

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