7WTO

Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-1 (without Rps2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The nucleoplasmic phase of pre-40S formation prior to nuclear export.

Cheng, J.Lau, B.Thoms, M.Ameismeier, M.Berninghausen, O.Hurt, E.Beckmann, R.

(2022) Nucleic Acids Res 50: 11924-11937

  • DOI: https://doi.org/10.1093/nar/gkac961
  • Primary Citation of Related Structures:  
    7WTN, 7WTO, 7WTP, 7WTQ, 7WTR, 7WTS, 7WTT, 7WTU, 7WTV, 7WTW, 7WTX, 7WTZ, 7WU0

  • PubMed Abstract: 

    Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.


  • Organizational Affiliation

    Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AB [auth SB]255Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AC [auth SE]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AD [auth SG]236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AE [auth SH]190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AF [auth SI]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AG [auth SJ]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AH [auth SL]156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13I [auth SN]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AJ [auth SO]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AK [auth SW]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AL [auth SX]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AM [auth SY]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AN [auth Sb]82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AO [auth Se]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1P [auth CA]274Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth C2]1,800Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Q [auth Sb]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references