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- EMDB-14925: Human TSEN with pre-tRNA-Tyr-GTA -

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Basic information

Entry
Database: EMDB / ID: EMD-14925
TitleHuman TSEN with pre-tRNA-Tyr-GTA
Map datamap
Sample
  • Complex: Human TSEN with pre-tRNA-Tyr-GTA
KeywordsRNP / endonuclease / tRNA / splicing / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSekulovski S / Trowitzsch S
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)TR 1711/1-7 Germany
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN.
Authors: Samoil Sekulovski / Lukas Sušac / Lukas S Stelzl / Robert Tampé / Simon Trowitzsch /
Abstract: Heterotetrameric human transfer RNA (tRNA) splicing endonuclease TSEN catalyzes intron excision from precursor tRNAs (pre-tRNAs), utilizing two composite active sites. Mutations in TSEN and its ...Heterotetrameric human transfer RNA (tRNA) splicing endonuclease TSEN catalyzes intron excision from precursor tRNAs (pre-tRNAs), utilizing two composite active sites. Mutations in TSEN and its associated RNA kinase CLP1 are linked to the neurodegenerative disease pontocerebellar hypoplasia (PCH). Despite the essential function of TSEN, the three-dimensional assembly of TSEN-CLP1, the mechanism of substrate recognition, and the structural consequences of disease mutations are not understood in molecular detail. Here, we present single-particle cryogenic electron microscopy reconstructions of human TSEN with intron-containing pre-tRNAs. TSEN recognizes the body of pre-tRNAs and pre-positions the 3' splice site for cleavage by an intricate protein-RNA interaction network. TSEN subunits exhibit large unstructured regions flexibly tethering CLP1. Disease mutations localize far from the substrate-binding interface and destabilize TSEN. Our work delineates molecular principles of pre-tRNA recognition and cleavage by human TSEN and rationalizes mutations associated with PCH.
History
DepositionMay 6, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14925.png

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Map

FileDownload / File: emd_14925.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.256 Å		1.06 Å/pix.
x 256 pix.
= 272.256 Å		1.06 Å/pix.
x 256 pix.
= 272.256 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-6.5722036 - 8.931126000000001
Average (Standard dev.)-0.0003101358 (±0.1524474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.256 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14925_msk_1.map
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Half map: half map A

Fileemd_14925_half_map_1.map
Annotationhalf_map_A
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Histogram (log scale)

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Half map: half map B

Fileemd_14925_half_map_2.map
Annotationhalf_map_B
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Sample components

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Entire : Human TSEN with pre-tRNA-Tyr-GTA

EntireName: Human TSEN with pre-tRNA-Tyr-GTA
Components
  • Complex: Human TSEN with pre-tRNA-Tyr-GTA

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Supramolecule #1: Human TSEN with pre-tRNA-Tyr-GTA

SupramoleculeName: Human TSEN with pre-tRNA-Tyr-GTA / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 81.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326518
FSC plot (resolution estimation)

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