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- EMDB-50488: Integrative Structure of the human intron lariat Spliceosome (ILS... -

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Basic information

Entry
Database: EMDB / ID: EMD-50488
TitleIntegrative Structure of the human intron lariat Spliceosome (ILS'') (Map 12)
Map data
Sample
  • Complex: human intron lariat spliceosome
KeywordsmRNA / splicing / intron lariat spliceosome / pre-mRNA
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.78 Å
AuthorsRothe P / Vorlaender MK / Plaschka C
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nature / Year: 2024
Title: Mechanism for the initiation of spliceosome disassembly.
Authors: Matthias K Vorländer / Patricia Rothe / Justus Kleifeld / Eric D Cormack / Lalitha Veleti / Daria Riabov-Bassat / Laura Fin / Alex W Phillips / Luisa Cochella / Clemens Plaschka /
Abstract: Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on ...Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on spliceosome assembly and remodelling for catalysis, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.
History
DepositionMay 29, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50488.png

Downloads & links

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Map

FileDownload / File: emd_50488.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 420 pix.
= 519.75 Å		1.24 Å/pix.
x 420 pix.
= 519.75 Å		1.24 Å/pix.
x 420 pix.
= 519.75 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.11996454 - 0.48032963
Average (Standard dev.)0.0027470572 (±0.022191135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 519.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_50488_additional_1.map
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AxesZYX

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Half map: #1

Fileemd_50488_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_50488_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : human intron lariat spliceosome

EntireName: human intron lariat spliceosome
Components
  • Complex: human intron lariat spliceosome

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Supramolecule #1: human intron lariat spliceosome

SupramoleculeName: human intron lariat spliceosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#14, #36, #15-#35, #2
Details: endogenous complex purified from K562 nuclear extract using a TFIP11-GFP tagged over-expression lent viral cell line.
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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 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: 4.78 Å / Number images used: 14635
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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