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- PDB-8ptw: Chaetomium thermophilum Rix1-complex -

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Basic information

Entry
Database: PDB / ID: 8ptw
TitleChaetomium thermophilum Rix1-complex
Components
  • Pre-rRNA-processing protein IPI3
  • Pre-rRNA-processing protein RIX1
KeywordsRIBOSOME / 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
Vps8 beta-propeller / WD repeat-containing protein WDR18/Ipi3/RID3 / Pre-rRNA-processing protein RIX1, N-terminal / rRNA processing/ribosome biogenesis / WD domain, G-beta repeat / Armadillo-type fold / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Pre-rRNA-processing protein IPI3 / Pre-rRNA-processing protein RIX1
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsThoms, M. / Cheng, J. / Denk, T. / Berninghausen, O. / Beckmann, R.
Funding supportEuropean Union, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
CT: Pre-rRNA-processing protein IPI3
CV: Pre-rRNA-processing protein RIX1
CU: Pre-rRNA-processing protein IPI3
CW: Pre-rRNA-processing protein RIX1


Theoretical massNumber of molelcules
Total (without water)264,9544
Polymers264,9544
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Pre-rRNA-processing protein IPI3


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 Pre-rRNA-processing protein RIX1


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chaetomium thermophilum Rix1-complex / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 43.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239033 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414568
ELECTRON MICROSCOPYf_angle_d0.72619922
ELECTRON MICROSCOPYf_dihedral_angle_d4.9372010
ELECTRON MICROSCOPYf_chiral_restr0.0472394
ELECTRON MICROSCOPYf_plane_restr0.0082544

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