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- EMDB-28755: Human tRNA Splicing Endonuclease Complex bound to 2'F-tRNA-Arg -

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Basic information

Entry
Database: EMDB / ID: EMD-28755
TitleHuman tRNA Splicing Endonuclease Complex bound to 2'F-tRNA-Arg
Map data
Sample
  • Complex: Human tRNA Splicing Endonuclease Complex bound to 2'F-pre-tRNA-ARG
Keywordssplicing endonuclease / pre-tRNA / TSEN / EndA / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsStanley RE / Hayne CK
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES102488 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES103206 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES102487 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZI ES043010 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES103326 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1K99-GM143534 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM136435 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex.
Authors: Cassandra K Hayne / Kevin John U Butay / Zachary D Stewart / Juno M Krahn / Lalith Perera / Jason G Williams / Robert M Petrovitch / Leesa J Deterding / A Gregory Matera / Mario J Borgnia / Robin E Stanley /
Abstract: Throughout bacteria, archaea and eukarya, certain tRNA transcripts contain introns. Pre-tRNAs with introns require splicing to form the mature anticodon stem loop. In eukaryotes, tRNA splicing is ...Throughout bacteria, archaea and eukarya, certain tRNA transcripts contain introns. Pre-tRNAs with introns require splicing to form the mature anticodon stem loop. In eukaryotes, tRNA splicing is initiated by the heterotetrameric tRNA splicing endonuclease (TSEN) complex. All TSEN subunits are essential, and mutations within the complex are associated with a family of neurodevelopmental disorders known as pontocerebellar hypoplasia (PCH). Here, we report cryo-electron microscopy structures of the human TSEN-pre-tRNA complex. These structures reveal the overall architecture of the complex and the extensive tRNA binding interfaces. The structures share homology with archaeal TSENs but contain additional features important for pre-tRNA recognition. The TSEN54 subunit functions as a pivotal scaffold for the pre-tRNA and the two endonuclease subunits. Finally, the TSEN structures enable visualization of the molecular environments of PCH-causing missense mutations, providing insight into the mechanism of pre-tRNA splicing and PCH.
History
DepositionNov 2, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28755.png

Downloads & links

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Map

FileDownload / File: emd_28755.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.607
Minimum - Maximum-1.5881478 - 3.048444
Average (Standard dev.)-0.0027165145 (±0.06947195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28755_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_28755_half_map_2.map
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Sample components

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Entire : Human tRNA Splicing Endonuclease Complex bound to 2'F-pre-tRNA-ARG

EntireName: Human tRNA Splicing Endonuclease Complex bound to 2'F-pre-tRNA-ARG
Components
  • Complex: Human tRNA Splicing Endonuclease Complex bound to 2'F-pre-tRNA-ARG

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Supramolecule #1: Human tRNA Splicing Endonuclease Complex bound to 2'F-pre-tRNA-ARG

SupramoleculeName: Human tRNA Splicing Endonuclease Complex bound to 2'F-pre-tRNA-ARG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Wild-type Human TSEN complex (TSEN34,TSEN54,TSEN2,TSEN15-His) bound to a synthetic 2'F-tRNA-Arg
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 192 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

BufferpH: 8
GridModel: Quantifoil R2/4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1557097
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 161512
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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