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- EMDB-50108: Medium-resolution cryo-EM structure of the Danio rerio tRNA ligas... -

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Basic information

Entry
Database: EMDB / ID: EMD-50108
TitleMedium-resolution cryo-EM structure of the Danio rerio tRNA ligase complex
Map data
Sample
  • Complex: tRNA ligase complex from D. rerio
KeywordstRNA ligase complex / RTCB / tRNA / tRNA maturation / tRNA splicing / LIGASE
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.32 Å
AuthorsChamera S / Zajko W / Czarnocki-Cieciura M / Jaciuk M / Koziej L / Nowak J / Wycisk K / Sroka M / Chramec-Glabik A / Smietanski M ...Chamera S / Zajko W / Czarnocki-Cieciura M / Jaciuk M / Koziej L / Nowak J / Wycisk K / Sroka M / Chramec-Glabik A / Smietanski M / Golebiowski F / Warminski M / Jemielity J / Glatt S / Nowotny M
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2019/33/B/NZ1/02839 Poland
CitationJournal: J Biol Chem / Year: 2025
Title: Structural and biochemical characterization of the 3'-5' tRNA splicing ligases.
Authors: Sebastian Chamera / Weronika Zajko / Mariusz Czarnocki-Cieciura / Marcin Jaciuk / Łukasz Koziej / Jakub Nowak / Krzysztof Wycisk / Małgorzata Sroka / Andrzej Chramiec-Głąbik / Mirosław ...Authors: Sebastian Chamera / Weronika Zajko / Mariusz Czarnocki-Cieciura / Marcin Jaciuk / Łukasz Koziej / Jakub Nowak / Krzysztof Wycisk / Małgorzata Sroka / Andrzej Chramiec-Głąbik / Mirosław Śmietański / Filip Gołębiowski / Marcin Warmiński / Jacek Jemielity / Sebastian Glatt / Marcin Nowotny /
Abstract: In archaea and metazoa, tRNA exons are ligated by the RNA ligases RtcB and RTCB, respectively. The metazoan RTCB forms a stable complex with four additional subunits, DDX1, FAM98B, CGI99, and ASHWIN. ...In archaea and metazoa, tRNA exons are ligated by the RNA ligases RtcB and RTCB, respectively. The metazoan RTCB forms a stable complex with four additional subunits, DDX1, FAM98B, CGI99, and ASHWIN. The role and assembly of these four components remain elusive. Furthermore, we lack structural information of how RNA substrates are recognized by 3'-5' tRNA ligases. Here, we use thiol-based chemical crosslinking to confirm the involvement of specific residues of RtcB in RNA binding, and we present a cryo-EM structure of the purified five-subunit Danio rerio tRNA ligase complex. The structure implies that the DDX1 helicase module is mobile and can modulate the activity of RTCB. Taken together, the presented results enhance our mechanistic understanding of RNA binding by 3'-5' tRNA splicing ligases and architecture of the metazoan tRNA ligase complex.
History
DepositionApr 16, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50108.png

Downloads & links

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Map

FileDownload / File: emd_50108.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.251
Minimum - Maximum-1.5201633 - 2.06766
Average (Standard dev.)0.0010379272 (±0.030590484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50108_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50108_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : tRNA ligase complex from D. rerio

EntireName: tRNA ligase complex from D. rerio
Components
  • Complex: tRNA ligase complex from D. rerio

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Supramolecule #1: tRNA ligase complex from D. rerio

SupramoleculeName: tRNA ligase complex from D. rerio / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 270 KDa

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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

Concentration0.2 mg/mL
BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35251
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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