9AXU

Non-translating S. pombe ribosome large subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.94 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

Ribosomes hibernate on mitochondria during cellular stress.

Gemin, O.Gluc, M.Rosa, H.Purdy, M.Niemann, M.Peskova, Y.Mattei, S.Jomaa, A.

(2024) Nat Commun 15: 8666-8666

  • DOI: https://doi.org/10.1038/s41467-024-52911-4
  • Primary Citation of Related Structures:  
    9AXT, 9AXU, 9AXV

  • PubMed Abstract: 

    Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42A [auth 0]106Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9UTI8 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43AB [auth 1]94Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9HGL8 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2CF [auth N]253Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT72 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3AG [auth O]388Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P40372 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4AH [auth P]363Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P35679 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18BI [auth Q]294Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74306 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6J [auth R]195Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P79071 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30CK [auth S]251Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O60143 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8L [auth T]259Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O13672 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6BM [auth U]189Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74905 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16AN [auth V]221Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q09127 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5AO [auth W]174Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT77 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13P [auth X]208Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74175 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14Q [auth Y]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15BR [auth Z]201Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9US22 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13AS [auth a]197Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O42848 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22AT [auth b]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14339 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18BU [auth c]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q8TFH1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19BV [auth d]193Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O42699 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20AW [auth e]176Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT68 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21BX [auth f]160Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O42706 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22Y [auth g]117Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q09668 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14BZ [auth h]139Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT61 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24BAA [auth i]149Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74884 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23ABA [auth j]141Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10330 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24CA [auth k]126Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P78946 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27ADA [auth l]136Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14388 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15BEA [auth m]148Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29FA [auth n]61Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q92366 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30AGA [auth o]109Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P52808 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31HA [auth p]113Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9URX6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32AIA [auth q]127Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33AJA [auth r]108Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9USX4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34BKA [auth s]111Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29LA [auth t]122Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36BMA [auth u]99Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37BNA [auth v]91Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38AOA [auth w]74Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39PA [auth x]51Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL28QA [auth y]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
ME [auth v],
RA [auth 0],
SA [auth 1]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 2]
AD [auth 2]
AE [auth 2]
BB [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Cancer SocietyUnited States--
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUNDGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection