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- EMDB-19789: Flexible reconstruction of the yeast U4/U6.U5 tri-snRNP (EMPIAR-1... -

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Basic information

Entry
Database: EMDB / ID: EMD-19789
TitleFlexible reconstruction of the yeast U4/U6.U5 tri-snRNP (EMPIAR-10073) using DynaMight
Map datalocal resolution filtered map from the DynaMight half maps. Reconstruction was done with a subset of 86,624 particles of EMPIAR-10073 with deformation correction
Sample
  • Complex: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
KeywordsSpliceosome / SPLICING
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsSchwab J / Scheres SHW
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
Citation
Journal: Nature / Year: 2016
Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
#1: Journal: Biorxiv
Title: DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images
Authors: Schwab J / Kimanius D / Burt A / Dendooven T / Scheres SHW
History
DepositionMar 5, 2024-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19789.png

Downloads & links

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Map

FileDownload / File: emd_19789.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map from the DynaMight half maps. Reconstruction was done with a subset of 86,624 particles of EMPIAR-10073 with deformation correction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 380 pix.
= 532.004 Å		1.4 Å/pix.
x 380 pix.
= 532.004 Å		1.4 Å/pix.
x 380 pix.
= 532.004 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.40001 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000815
Minimum - Maximum-0.0038367247 - 0.007369961
Average (Standard dev.)0.000006756027 (±0.00009934307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 532.0038 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Unfiltered half map obtained with DynaMight reconstruction

Fileemd_19789_half_map_1.map
AnnotationUnfiltered half map obtained with DynaMight reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map obtained with DynaMight reconstruction

Fileemd_19789_half_map_2.map
AnnotationUnfiltered half map obtained with DynaMight reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP

EntireName: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
Components
  • Complex: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP

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Supramolecule #1: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP

SupramoleculeName: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 140155
Startup modelType of model: EMDB MAP
EMDB ID:

2966

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86624
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)

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