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- EMDB-18239: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and... -

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Basic information

Entry
Database: EMDB / ID: EMD-18239
TitleStructure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6)
Map datasharpened map
Sample
  • Complex: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6)
KeywordsU5 snRNP / CD2BP2 / TSSC4 / spliceosome / splicing
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsRiabov Bassat D / Plaschka C / Vorlaender MK
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC- 2020-STG 949081European Union
H2020 Marie Curie Actions of the European Commission101028744European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of human U5 snRNP late biogenesis and recycling.
Authors: Daria Riabov Bassat / Supapat Visanpattanasin / Matthias K Vorländer / Laura Fin / Alexander W Phillips / Clemens Plaschka /
Abstract: Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP ...Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP is the ~1 MDa 'heart' of the spliceosome and is recycled through an unknown mechanism involving major architectural rearrangements and the dedicated chaperones CD2BP2 and TSSC4. Late steps in U5 snRNP biogenesis similarly involve these chaperones. Here we report cryo-electron microscopy structures of four human U5 snRNP-CD2BP2-TSSC4 complexes, revealing how a series of molecular events primes the U5 snRNP to generate the ~2 MDa U4/U6.U5 tri-snRNP, the largest building block of the spliceosome.
History
DepositionAug 17, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18239.png

Downloads & links

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Map

FileDownload / File: emd_18239.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.7047431 - 4.129713
Average (Standard dev.)0.0024980432 (±0.062094074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 446.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_18239_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_18239_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_18239_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and...

EntireName: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6)
Components
  • Complex: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6)

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Supramolecule #1: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and...

SupramoleculeName: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 and TSSC4 (Map 6)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1 MDa

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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: 7.9
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: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6qw6

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 256427
FSC plot (resolution estimation)

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