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- EMDB-62844: Cryo-EM structure of the thermophile spliceosome (state B*Q2 focu... -

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Basic information

Entry
Database: EMDB / ID: EMD-62844
TitleCryo-EM structure of the thermophile spliceosome (state B*Q2 focus DHX15)
Map dataconsensus refined map without post processing
Sample
  • Complex: spliceosome in state B*Q2
KeywordsSpilceosome / DHX15 / DHX35 / GPATCH1 / SPLICING
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi Y / Fischer P / Wang M / Yuan R / Meng W / Luehrmann R / Lau B / Hurt E / Cheng J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2025
Title: Structural insights into spliceosome fidelity: DHX35-GPATCH1- mediated rejection of aberrant splicing substrates.
Authors: Yi Li / Paulina Fischer / Mengjiao Wang / Qianxing Zhou / Aixia Song / Rui Yuan / Wanyu Meng / Fei Xavier Chen / Reinhard Lührmann / Benjamin Lau / Ed Hurt / Jingdong Cheng /
Abstract: The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights into the step-wise ...The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights into the step-wise assembly, catalytic splicing and final disassembly of the spliceosome. However, the molecular details of how the spliceosome recognizes and rejects suboptimal splicing substrates remained unclear. Here, we show cryo-electron microscopy structures of spliceosomal quality control complexes from a thermophilic eukaryote, Chaetomium thermophilum. The spliceosomes, henceforth termed B*, are stalled at a catalytically activated state but prior to the first splicing reaction due to an aberrant 5' splice site conformation. This state is recognized by G-patch protein GPATCH1, which is docked onto PRP8-EN and -RH domains and has recruited the cognate DHX35 helicase to its U2 snRNA substrate. In B*, DHX35 has dissociated the U2/branch site helix, while the disassembly helicase DHX15 is docked close to its U6 RNA 3'-end substrate. Our work thus provides mechanistic insights into the concerted action of two spliceosomal helicases in maintaining splicing fidelity by priming spliceosomes that are bound to aberrant splice substrates for disassembly.
History
DepositionDec 23, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62844.png

Downloads & links

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Map

FileDownload / File: emd_62844.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus refined map without post processing
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 447.36 Å		0.93 Å/pix.
x 480 pix.
= 447.36 Å		0.93 Å/pix.
x 480 pix.
= 447.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.021544391 - 0.048232578
Average (Standard dev.)0.000094199786 (±0.0023196908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 447.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local resolution filtered map using Relion

Fileemd_62844_additional_1.map
Annotationlocal resolution filtered map using Relion
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: multibody refined map focusing on the body region...

Fileemd_62844_additional_2.map
Annotationmultibody refined map focusing on the body region and local resolution filtered using Relion
Projections & Slices
AxesZYX

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Histogram

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Additional map: multibody refined map focusing on the SYF1 region...

Fileemd_62844_additional_3.map
Annotationmultibody refined map focusing on the SYF1 region and local resolution filtered using Relion
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_62844_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62844_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : spliceosome in state B*Q2

EntireName: spliceosome in state B*Q2
Components
  • Complex: spliceosome in state B*Q2

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Supramolecule #1: spliceosome in state B*Q2

SupramoleculeName: spliceosome in state B*Q2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#39
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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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: FEI FALCON IV (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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6817

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9744
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
Final angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
FSC plot (resolution estimation)

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