[English] 日本語
![](img/lk-miru.gif)
- EMDB-17903: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 in... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D | |||||||||
![]() | Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D - local resolution filtered | |||||||||
![]() |
| |||||||||
![]() | biogenesis / pre-60S / 5S RNP / RIBOSOME | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.79 Å | |||||||||
![]() | Thoms M / Cheng J / Denk T / Berninghausen O / Beckmann R | |||||||||
Funding support | European Union, 1 items
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 7.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 22.9 KB 22.9 KB | Display Display | ![]() |
Images | ![]() | 113.7 KB | ||
Filedesc metadata | ![]() | 4.1 KB | ||
Others | ![]() ![]() ![]() | 239 MB 442.3 MB 442.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ptwC ![]() 8puwC ![]() 8pv1C ![]() 8pv2C ![]() 8pv3C ![]() 8pv4C ![]() 8pv5C ![]() 8pv6C ![]() 8pv7C ![]() 8pv8C ![]() 8pvkC ![]() 8pvlC C: citing same article ( |
---|
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D - local resolution filtered | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation...
File | emd_17903_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation...
File | emd_17903_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D - half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation...
File | emd_17903_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D - half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 in...
Entire | Name: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D |
---|---|
Components |
|
-Supramolecule #1: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 in...
Supramolecule | Name: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#60 |
---|---|
Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / 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 |
-
Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74129 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |