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- EMDB-16950: cryo-EM structure of human tRNA(AspGUC) -

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Basic information

Entry
Database: EMDB / ID: EMD-16950
Titlecryo-EM structure of human tRNA(AspGUC)
Map datamain map
Sample
  • Complex: free Asp tRNA
KeywordstRNA / human / RNA
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.26 Å
AuthorsBiela AP
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
CitationJournal: EMBO J / Year: 2025
Title: Determining the effects of pseudouridine incorporation on human tRNAs.
Authors: Anna D Biela / Jakub S Nowak / Artur P Biela / Sunandan Mukherjee / Seyed Naeim Moafinejad / Satyabrata Maiti / Andrzej Chramiec-Głąbik / Rahul Mehta / Jakub Jeżowski / Dominika Dobosz / ...Authors: Anna D Biela / Jakub S Nowak / Artur P Biela / Sunandan Mukherjee / Seyed Naeim Moafinejad / Satyabrata Maiti / Andrzej Chramiec-Głąbik / Rahul Mehta / Jakub Jeżowski / Dominika Dobosz / Priyanka Dahate / Veronique Arluison / Frank Wien / Paulina Indyka / Michal Rawski / Janusz M Bujnicki / Ting-Yu Lin / Sebastian Glatt /
Abstract: Transfer RNAs (tRNAs) are ubiquitous non-coding RNA molecules required to translate mRNA-encoded sequence information into nascent polypeptide chains. Their relatively small size and heterogenous ...Transfer RNAs (tRNAs) are ubiquitous non-coding RNA molecules required to translate mRNA-encoded sequence information into nascent polypeptide chains. Their relatively small size and heterogenous patterns of their RNA modifications have impeded the systematic structural characterization of individual tRNAs. Here, we use single-particle cryo-EM to determine the structures of four human tRNAs before and after incorporation of pseudouridines (Ψ). Following post-transcriptional modifications by distinct combinations of human pseudouridine synthases, we find that tRNAs become stabilized and undergo specific local structural changes. We establish interactions between the D- and T-arms as the key linchpin in the tertiary structure of tRNAs. Our structures of human tRNAs highlight the vast potential of cryo-EM combined with biophysical measurements and computational simulations for structure-function analyses of tRNAs and other small, folded RNA domains.
History
DepositionMar 30, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16950.png

Downloads & links

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Map

FileDownload / File: emd_16950.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 128 pix.
= 216.576 Å		1.69 Å/pix.
x 128 pix.
= 216.576 Å		1.69 Å/pix.
x 128 pix.
= 216.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.692 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.36
Minimum - Maximum-2.9378383 - 5.4544363
Average (Standard dev.)0.010011033 (±0.1694268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 216.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_16950_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_16950_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : free Asp tRNA

EntireName: free Asp tRNA
Components
  • Complex: free Asp tRNA

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Supramolecule #1: free Asp tRNA

SupramoleculeName: free Asp tRNA / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Details: 8mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 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) / Number grids imaged: 1 / Number real images: 6765 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 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: 706586
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 5.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 85573
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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