9FO0 | pdb_00009fo0

PF30S ribosomal subunit - control

  • Classification: TRANSLATION
  • Organism(s): Pyrococcus furiosus
  • Mutation(s): No 

  • Deposited: 2024-06-11 Released: 2025-01-15 
  • Deposition Author(s): Hassan, A.H., Demo, G.
  • Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, European Union (EU)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization.

Hassan, A.H.Pinkas, M.Yaeshima, C.Ishino, S.Uchiumi, T.Ito, K.Demo, G.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkae1324
  • Primary Citation of Related Structures:  
    9FNY, 9FNZ, 9FO0

  • PubMed Abstract: 

    Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various ribosome-interacting proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms to adapt to stress. Despite extensive studies on bacteria and eukaryotes, understanding factor-mediated ribosome dimerization or anti-association in archaea remains elusive. Here, we present cryo-electron microscopy structures of an archaeal 30S dimer complexed with an archaeal ribosome dimerization factor (designated aRDF), from Pyrococcus furiosus, resolved at a resolution of 3.2 Å. The complex features two 30S subunits stabilized by aRDF homodimers in a unique head-to-body architecture, which differs from the disome architecture observed during hibernation in bacteria and eukaryotes. aRDF interacts directly with eS32 ribosomal protein, which is essential for subunit association. The binding mode of aRDF elucidates its anti-association properties, which prevent the assembly of archaeal 70S ribosomes.


  • Organizational Affiliation
    • Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding proteinA [auth A1]60Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8TZM6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS32B [auth A2]37Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U232 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8C [auth A5]123Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2E [auth AB]202Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U0F0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3F [auth AC]210Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U004 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1G [auth AD]198Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8TZE1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4H [auth AE]180Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for P61993 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4I [auth AF]243Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U011 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5J [auth AG]236Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U017 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6K [auth AH]125Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U3H8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7L [auth AI]215Pyrococcus furiosusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8M [auth AJ]130Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U014 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8N [auth AK]127Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U1Y5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9O [auth AL]135Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U0E7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10P [auth AM]102Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for P61885 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11Q [auth AN]137Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U0E3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12R [auth AO]147Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for P61995 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13S [auth AP]148Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U0E2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14T [auth AQ]56Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U013 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15U [auth AR]158Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8TZD9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17V [auth AS]113Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U008 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17W [auth AT]67Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U0U1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19X [auth AU]132Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U002 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19Y [auth AV]150Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U0T4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24Z [auth AW]99Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U442 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS31AA [auth AX]50Pyrococcus furiosusMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27BA [auth AY]63Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U474 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28CA [auth AZ]71Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U159 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 4
MoleculeChains LengthOrganismImage
16S rRNAD [auth AA]1,495Pyrococcus furiosus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLL2008
European Union (EU)European UnionLX22NPO5103

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references