+Open data
-Basic information
Entry | Database: PDB / ID: 8ptw | ||||||
---|---|---|---|---|---|---|---|
Title | Chaetomium thermophilum Rix1-complex | ||||||
Components |
| ||||||
Keywords | RIBOSOME / biogenesis / pre-60S / 5S RNP | ||||||
Function / homology | Function and homology information rixosome complex / nuclear pre-replicative complex / DNA-templated DNA replication / rRNA processing / nucleus Similarity search - Function | ||||||
Biological species | Thermochaetoides thermophila DSM 1495 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å | ||||||
Authors | Thoms, M. / Cheng, J. / Denk, T. / Berninghausen, O. / Beckmann, R. | ||||||
Funding support | European Union, 1items
| ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ptw.cif.gz | 325.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ptw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ptw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ptw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ptw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8ptw_validation.xml.gz | 55.9 KB | Display | |
Data in CIF | 8ptw_validation.cif.gz | 84.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/8ptw ftp://data.pdbj.org/pub/pdb/validation_reports/pt/8ptw | HTTPS FTP |
-Related structure data
Related structure data | 17879MC 8puwC 8pv1C 8pv2C 8pv3C 8pv4C 8pv5C 8pv6C 8pv7C 8pv8C 8pvkC 8pvlC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 47627.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S1T5 #2: Protein | Mass: 84849.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S5R0 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Chaetomium thermophilum Rix1-complex / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 43.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239033 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|