9RVU | pdb_00009rvu

in situ S. pombe hibernating ribosome after 7 days of glucose depletion


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

SNOR promotes translation restart after dormancy.

Gluc, M.Rosa, H.Bozko, M.Turner, L.A.Prince, C.R.Peskova, Y.Feaga, H.A.Gould, K.L.Mattei, S.Jomaa, A.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10530-7
  • Primary Citation Related Structures: 
    9PHC, 9RVU

  • PubMed Abstract: 

    Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis 1-4 . How inactive eukaryotic ribosomes are reactivated when nutrients return remains unclear. Here, using high-resolution in situ cryo-electron tomography in Schizosaccharomyces pombe, we identify SNOR, an SBDS domain-containing ribosome-associated factor that binds at the peptidyl transferase centre and contacts the hypusinated loop of eIF5A during glucose depletion-induced dormancy. Rather than acting as a canonical hibernation factor, SNOR licenses dormant ribosomes for rapid translational restart. Upon glucose repletion, SNOR and eIF5A act together to promote efficient recovery of polysomes and exit from dormancy. These findings define a stress-responsive ribosome restart module that couples carbon-source limitation to surveillance of the ribosomal active site and reactivation of protein synthesis.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, University of Virginia, Charlottesville, VA, USA.

Macromolecule Content 

  • Total Structure Weight: 3,370.7 kDa 
  • Atom Count: 209,623 
  • Modeled Residue Count: 17,579 
  • Deposited Residue Count: 19,207 
  • Unique protein chains: 79
  • Unique nucleic acid chains: 4

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
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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
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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
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11AP [auth AR]139Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19BQ [auth AS]154Schizosaccharomyces pombeMutation(s): 0 
UniProt
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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 uS13AT [auth AV]152Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P0CT66 (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
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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
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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
Find proteins for Q9UTG4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27CA [auth Ah]83Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74330 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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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
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS30AFA [auth Ak]61Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1GA [auth Am]314Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42HA [auth B0]106Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43AIA [auth B1]94Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2AMA [auth BN]253Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3ANA [auth BO]388Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4AOA [auth BP]363Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18BPA [auth BQ]294Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6QA [auth BR]195Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30CRA [auth BS]251Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8SA [auth BT]259Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16ATA [auth BV]221Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5AUA [auth BW]174Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13VA [auth BX]208Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14WA [auth BY]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15BXA [auth BZ]201Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13AYA [auth Ba]197Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18BZA [auth Bc]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19BAB [auth Bd]193Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20ABB [auth Be]176Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21BCB [auth Bf]160Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22DB [auth Bg]117Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14AEB [auth Bh]139Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24BFB [auth Bi]149Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23AGB [auth Bj]141Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24HB [auth Bk]126Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27AIB [auth Bl]136Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15BJB [auth Bm]148Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29KB [auth Bn]61Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30ALB [auth Bo]109Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31MB [auth Bp]113Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32ANB [auth Bq]127Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33AOB [auth Br]108Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34BPB [auth Bs]111Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29QB [auth Bt]122Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36BRB [auth Bu]99Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37BSB [auth Bv]91Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38ATB [auth Bw]74Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39UB [auth Bx]51Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL28VB [auth By]134Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome-associated protein oga1WB [auth H1]284Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor 2XB [auth HE]842Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1BYB [auth HL]216Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains  Sequence LengthOrganismDetailsImage
SDO1-like protein C21C3.19ZB [auth HS]106Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9P7K6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 79
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A-1AC [auth HI]157Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40ABC [auth BA]51Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6BCC [auth BU]189Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22ADC [auth Bb]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22AEC [auth A]20Schizosaccharomyces pombeMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S small subunit ribosomal RNAA [auth AA]1,842Schizosaccharomyces pombe
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Entity ID: 36
MoleculeChains LengthOrganismImage
28S large subunit ribosomal RNAJA [auth B2]3,498Schizosaccharomyces pombe
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Entity ID: 37
MoleculeChains LengthOrganismImage
5S large subunit ribosomal RNAKA [auth B3]246Schizosaccharomyces pombe
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Entity ID: 38
MoleculeChains LengthOrganismImage
5.8S large subunit ribosomal RNALA [auth B4]165Schizosaccharomyces pombe
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONWarp2.0.0dev36

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-01
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-27
    Changes: Data collection, Database references