7OHT

Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors.

Poll, G.Pilsl, M.Griesenbeck, J.Tschochner, H.Milkereit, P.

(2021) PLoS One 16: e0252497-e0252497

  • DOI: https://doi.org/10.1371/journal.pone.0252497
  • Primary Citation of Related Structures:  
    7OF1, 7OH3, 7OHP, 7OHQ, 7OHR, 7OHS, 7OHT, 7OHU, 7OHV, 7OHW, 7OHX, 7OHY

  • PubMed Abstract: 

    In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits.


  • Organizational Affiliation

    Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3D [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AE [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5F [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AG [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AH [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AI [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-A174Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AK [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AL [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AM [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AN [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AO [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AP [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4Q [auth W]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1R [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32S [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AT [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2U [auth m]486Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2V [auth r]261Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24W [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RPF2X [auth v]344Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of ribosome biosynthesisY [auth w]203Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly protein 4Z [auth x]515Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6AA [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S rRNAA [auth 1]3,396Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S rRNAB [auth 2]158Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth 3]121Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE1.1
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 960

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 2.0: 2021-11-10
    Changes: Atomic model, Data collection
  • Version 2.1: 2021-12-08
    Changes: Database references