9PHC | pdb_00009phc

In vitro reconstituted complex of purified S. pombe large ribosomal subunit and SNOR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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: 2,019.22 kDa 
  • Atom Count: 122,816 
  • Modeled Residue Count: 9,665 
  • Deposited Residue Count: 10,601 
  • Unique protein chains: 41
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42A [auth B0]106Schizosaccharomyces pombe 972h-Mutation(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 B1]94Schizosaccharomyces pombe 972h-Mutation(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 BN]253Schizosaccharomyces pombe 972h-Mutation(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 BO]388Schizosaccharomyces pombe 972h-Mutation(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 BP]363Schizosaccharomyces pombe 972h-Mutation(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 BQ]294Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6J [auth BR]195Schizosaccharomyces pombe 972h-Mutation(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 BS]251Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8L [auth BT]259Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6BM [auth BU]189Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16AN [auth BV]221Schizosaccharomyces pombe 972h-Mutation(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 BW]174Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13P [auth BX]208Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14Q [auth BY]134Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15BR [auth BZ]201Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13AS [auth Ba]197Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22AT [auth Bb]187Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18BU [auth Bc]187Schizosaccharomyces pombe 972h-Mutation(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 Bd]193Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20AW [auth Be]176Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21BX [auth Bf]160Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22Y [auth Bg]117Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14BZ [auth Bh]139Schizosaccharomyces pombe 972h-Mutation(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 Bi]149Schizosaccharomyces pombe 972h-Mutation(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 Bj]141Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24CA [auth Bk]126Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27ADA [auth Bl]136Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15BEA [auth Bm]148Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29FA [auth Bn]61Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30AGA [auth Bo]109Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31HA [auth Bp]113Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32AIA [auth Bq]127Schizosaccharomyces pombe 972h-Mutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33AJA [auth Br]108Schizosaccharomyces pombe 972h-Mutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34BKA [auth Bs]111Schizosaccharomyces pombe 972h-Mutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29LA [auth Bt]122Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36BMA [auth Bu]99Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37BNA [auth Bv]91Schizosaccharomyces pombe 972h-Mutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38AOA [auth Bw]74Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39PA [auth Bx]51Schizosaccharomyces pombe 972h-Mutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL28QA [auth By]134Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
SDO1-like protein C21C3.19RA [auth HS]106Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: SPBC21C3.19
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Entity ID: 3
MoleculeChains LengthOrganismImage
28S ribosomal RNAC [auth B2]3,498Schizosaccharomyces pombe 972h-
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S ribosomal RNAD [auth B3]246Schizosaccharomyces pombe 972h-
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Entity ID: 5
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAE [auth B4]165Schizosaccharomyces pombe 972h-
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION3

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: 2026-04-15
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-27
    Changes: Data collection, Database references