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- EMDB-55721: Cryo-EM structure of nTr20 tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-55721
TitleCryo-EM structure of nTr20 tRNA
Map dataCryo-EM structure of nTr20-tRNA
Sample
  • Organelle or cellular component: tRNA molecule
    • RNA: nTr20 tRNA
Keywordstransfer-RNA. nTr20 / neuronal tRNA / RNA
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 Å
AuthorsMehta R / Glatt S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Solid-state nanopore sensing reveals conformational changes induced by a mutation in a neuron-specific tRNAArg.
Authors: Shankar Dutt / Lien B Lai / Rahul Mehta / Buddini I Karawdeniya / Y M Nuwan D Y Bandara / Andrew J Clulow / Sebastian Glatt / Venkat Gopalan / Patrick Kluth /
Abstract: We demonstrate that solid-state nanopore sensing is a powerful single-molecule method for analyzing RNA conformational ensembles. As a model, we employed n-Tr20, a neuron-specific cytoplasmic tRNA$_ ...We demonstrate that solid-state nanopore sensing is a powerful single-molecule method for analyzing RNA conformational ensembles. As a model, we employed n-Tr20, a neuron-specific cytoplasmic tRNA$_{\mathrm{UCU}}^{\mathrm{Arg}}$, whose C50U mutation is associated with neurodegeneration in C57BL/6J mice. Maturation of the n-Tr20$^{\mathrm{C50U}}$ precursor is impaired as the mutation stabilizes a conformational ensemble different from the wild type. To gain insights into how this mutation engenders structural differences, we used solid-state nanopore sensing for the real-time identification of metastable conformers that are not easily observable by ensemble methods. Ion-current traces recorded using an 8 nm nanopore revealed broad contours of the conformational landscape of n-Tr20/n-Tr20$^\mathrm{C50U}$  $\pm$ Mg$^{2+}$. Additionally, cryo-electron microscopy analysis and small-angle X-ray scattering studies revealed structural plasticity consistent with the nanopore-sensing data. Since dynamics undergird RNA (dys)function in cellular physiology and pathology, nanopore sensing to determine RNA conformational sampling is a valuable addition to the growing RNA structural analysis toolkit.
History
DepositionNov 15, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55721.png

Downloads & links

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Map

FileDownload / File: emd_55721.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of nTr20-tRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 288 pix.
= 247.68 Å		0.86 Å/pix.
x 288 pix.
= 247.68 Å		0.86 Å/pix.
x 288 pix.
= 247.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.044909135 - 0.20602097
Average (Standard dev.)0.001253713 (±0.0086588785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 247.68001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55721_msk_1.map
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Additional map: Cryo-EM structure of nTr20-tRNA conformation 2

Fileemd_55721_additional_1.map
AnnotationCryo-EM structure of nTr20-tRNA conformation 2
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Additional map: Cryo-EM structure of nTr20-tRNA conformation 3

Fileemd_55721_additional_2.map
AnnotationCryo-EM structure of nTr20-tRNA conformation 3
Projections & Slices
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Half map: #1

Fileemd_55721_half_map_1.map
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Half map: #2

Fileemd_55721_half_map_2.map
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Sample components

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Entire : tRNA molecule

EntireName: tRNA molecule
Components
  • Organelle or cellular component: tRNA molecule
    • RNA: nTr20 tRNA

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Supramolecule #1: tRNA molecule

SupramoleculeName: tRNA molecule / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in-vitro synthesized
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23 KDa

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Macromolecule #1: nTr20 tRNA

MacromoleculeName: nTr20 tRNA / type: rna / ID: 1
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GUCUCUGUGG CGCAAUGGAC GAGCGCGCUG GACUUCUAAU CCAGAGGUUC CGGGUUCGAG UCCCGGCAGA GAUG

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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

Concentration0.0011 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium Chloride
50.0 mMKClPottasium chloride
1.0 mMMgCl2Magnesium Chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1035336 / Details: blob picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 31561
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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