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- EMDB-17895: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with R... -

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Entry
Database: EMDB / ID: EMD-17895
TitleChaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2
Map dataChaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2 - local resolution filtered
Sample
  • Complex: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2
Keywordsbiogenesis / pre-60S / 5S RNP / RIBOSOME
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsThoms M / Cheng J / Denk T / Berninghausen O / Beckmann R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO Rep / Year: 2023
Title: Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Authors: Matthias Thoms / Benjamin Lau / Jingdong Cheng / Lisa Fromm / Timo Denk / Nikola Kellner / Dirk Flemming / Paulina Fischer / Laurent Falquet / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from ...The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180° rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.
History
DepositionJul 15, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17895.png

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Map

FileDownload / File: emd_17895.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2 - local resolution filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 500 pix.
= 522.5 Å		1.05 Å/pix.
x 500 pix.
= 522.5 Å		1.05 Å/pix.
x 500 pix.
= 522.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.1539822 - 3.904291
Average (Standard dev.)0.0007918114 (±0.037827477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 522.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Chaetomium thermophilum pre-60S State 3 - post-5S rotation...

Fileemd_17895_additional_1.map
AnnotationChaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: Chaetomium thermophilum pre-60S State 3 - post-5S rotation...

Fileemd_17895_half_map_1.map
AnnotationChaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2 - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Chaetomium thermophilum pre-60S State 3 - post-5S rotation...

Fileemd_17895_half_map_2.map
AnnotationChaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2 - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetomium thermophilum pre-60S State 3 - post-5S rotation with R...

EntireName: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2
Components
  • Complex: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2

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Supramolecule #1: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with R...

SupramoleculeName: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#62
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25753
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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