7OH3

Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 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
rRNA-processing protein CGR1D [auth 5]120Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AE [auth A]254Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3F [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AG [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5H [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AI [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AJ [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AK [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AL [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AM [auth J]174Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AN [auth L]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AO [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AP [auth N]204Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AQ [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AR [auth P]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AS [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AT [auth R]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AU [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AV [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AW [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AX [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4Y [auth W]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25Z [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AAA [auth Y]127Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ABA [auth Z]136Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28CA [auth a]149Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1DA [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30EA [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AFA [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32GA [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AHA [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AIA [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AJA [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AKA [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ALA [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38MA [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39NA [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 2OA [auth m]486Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-APA [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2QA [auth r]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear GTP-binding protein NUG1RA [auth s]520Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24SA [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RPF2TA [auth v]344Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of ribosome biosynthesisUA [auth w]203Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly protein 4VA [auth x]515Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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UniProt GroupP25382
Sequence Annotations
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6WA [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12522
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UniProt GroupQ12522
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0642 protein YBL028CXA [auth z]106Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38202 
Go to UniProtKB:  P38202
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UniProt GroupP38202
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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: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTISOLDE1.1

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
  • Version 2.2: 2024-07-10
    Changes: Data collection, Refinement description