9AXT

Non-translating S. pombe ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2AB [auth AD]292Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9Y7L8 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1BC [auth AE]252Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94438 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5D [auth AF]253Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74892 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3E [auth AG]249Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O60128 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4CF [auth AH]262Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9P4W9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7AG [auth AI]203Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14277 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6BH [auth AJ]239Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9C0Z7 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7I [auth AK]195Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10101 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8BJ [auth AL]200Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9P7B2 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4BK [auth AM]192Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O59675 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS10BL [auth AN]147Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O13614 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17AM [auth AO]152Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT74 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12AN [auth AP]145Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14062 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15O [auth AQ]151Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P28189 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11BP [auth AR]139Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT57 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19BQ [auth AS]154Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9UTQ6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9AR [auth AT]140Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT64 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17AS [auth AU]131Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O42984 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13BT [auth AV]152Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT67 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19AU [auth AW]144Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P58234 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10V [auth Aa]118Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74893 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21W [auth Ab]87Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P05764 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8AX [auth Ac]130Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT58 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12AY [auth Ad]143Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT75 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24AZ [auth Ae]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25AAA [auth Af]89Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P79009 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26BBA [auth Ag]119Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27CA [auth Ah]83Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28ADA [auth Ai]68Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14EA [auth Aj]56Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74329 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS30BFA [auth Ak]61Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT63 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42GA [auth B0]106Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43AHA [auth B1]94Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2CLA [auth BN]253Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3AMA [auth BO]388Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4ANA [auth BP]363Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18BOA [auth BQ]294Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74306 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6PA [auth BR]195Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P79071 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30CQA [auth BS]251Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O60143 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8RA [auth BT]259Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O13672 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6BSA [auth BU]189Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74905 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16ATA [auth BV]221Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q09127 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5AUA [auth BW]174Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT77 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13VA [auth BX]208Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74175 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14WA [auth BY]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94238 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15BXA [auth BZ]201Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9US22 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13AYA [auth Ba]197Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O42848 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22AZA [auth Bb]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14339 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18BAB [auth Bc]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q8TFH1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19BBB [auth Bd]193Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O42699 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20ACB [auth Be]176Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT68 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21BDB [auth Bf]160Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O42706 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22EB [auth Bg]117Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q09668 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14BFB [auth Bh]139Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT61 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24BGB [auth Bi]149Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74884 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23AHB [auth Bj]141Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10330 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24IB [auth Bk]126Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P78946 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27AJB [auth Bl]136Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14388 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15BKB [auth Bm]148Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P57728 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29LB [auth Bn]61Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q92366 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30AMB [auth Bo]109Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P52808 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31NB [auth Bp]113Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9URX6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32AOB [auth Bq]127Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P79015 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33APB [auth Br]108Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9USX4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34BQB [auth Bs]111Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9URT8 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29RB [auth Bt]122Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74904 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36BSB [auth Bu]99Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94658 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37BTB [auth Bv]91Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P05733 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38AUB [auth Bw]74Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9USR7 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39VB [auth Bx]51Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P05767 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL28WB [auth By]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14069 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
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