6YLE

Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.

Kater, L.Mitterer, V.Thoms, M.Cheng, J.Berninghausen, O.Beckmann, R.Hurt, E.

(2020) Mol Cell 79: 615-628.e5

  • DOI: https://doi.org/10.1016/j.molcel.2020.06.032
  • Primary Citation of Related Structures:  
    6YLE, 6YLF, 6YLG, 6YLH, 6YLX, 6YLY

  • PubMed Abstract: 

    Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1 2 -Ipi3 2 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.


  • Organizational Affiliation

    Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein IPI3
A, B
555Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53877 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53877 
Go to UniProtKB:  P53877
Entity Groups  
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UniProt GroupP53877
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein RIX1
C, D
763Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38883 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38883 
Go to UniProtKB:  P38883
Entity Groups  
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UniProt GroupP38883
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein IPI1E [auth K]334Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38803 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38803 
Go to UniProtKB:  P38803
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38803
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0.8

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references