8PTW | pdb_00008ptw

Chaetomium thermophilum Rix1-complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8PTW

This is version 1.1 of the entry. See complete history

Literature

Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.

Thoms, M.Lau, B.Cheng, J.Fromm, L.Denk, T.Kellner, N.Flemming, D.Fischer, P.Falquet, L.Berninghausen, O.Beckmann, R.Hurt, E.

(2023) EMBO Rep 24: e57984-e57984

  • DOI: https://doi.org/10.15252/embr.202357984
  • Primary Citation Related Structures: 
    8PTW, 8PUW, 8PV1, 8PV2, 8PV3, 8PV4, 8PV5, 8PV6, 8PV7, 8PV8, 8PVK, 8PVL

  • PubMed 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 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.


  • Organizational Affiliation
    • Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.

Macromolecule Content 

  • Total Structure Weight: 264.95 kDa 
  • Atom Count: 14,242 
  • Modeled Residue Count: 1,878 
  • Deposited Residue Count: 2,436 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein IPI3A [auth CT],
C [auth CU]
437Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S1T5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S1T5 
Go to UniProtKB:  G0S1T5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S1T5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein RIX1B [auth CV],
D [auth CW]
781Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S5R0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S5R0 
Go to UniProtKB:  G0S5R0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S5R0
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references