9FNZ | pdb_00009fnz

PF30S-PF30S dimer mediated by aRDF from P. furiosus (Structure II)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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],
FA [auth B1]
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],
GA [auth B2]
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
Archaeal Ribosome Dimerizing Factor (aRDF)C [auth A3],
D [auth A4],
HA [auth B3],
IA [auth B4]
306Pyrococcus furiosusMutation(s): 0 
Gene Names: PF0560
UniProt
Find proteins for Q8U3B0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8E [auth A5],
JA [auth B5]
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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2G [auth AB],
LA [auth BB]
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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3H [auth AC],
MA [auth BC]
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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1I [auth AD],
NA [auth BD]
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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4J [auth AE],
OA [auth BE]
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: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4K [auth AF],
PA [auth BF]
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: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5L [auth AG],
QA [auth BG]
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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6M [auth AH],
RA [auth BH]
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: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7N [auth AI],
SA [auth BI]
215Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U0M8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8O [auth AJ],
TA [auth BJ]
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: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8P [auth AK],
UA [auth BK]
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: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9Q [auth AL],
VA [auth BL]
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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10R [auth AM],
WA [auth BM]
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: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11S [auth AN],
XA [auth BN]
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: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12T [auth AO],
YA [auth BO]
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: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13U [auth AP],
ZA [auth BP]
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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14AB [auth BQ],
V [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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15BB [auth BR],
W [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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17CB [auth BS],
X [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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17DB [auth BT],
Y [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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19EB [auth BU],
Z [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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19AA [auth AV],
FB [auth BV]
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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24BA [auth AW],
GB [auth BW]
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: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS31CA [auth AX],
HB [auth BX]
50Pyrococcus furiosusMutation(s): 0 
UniProt
Find proteins for Q8U443 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27DA [auth AY],
IB [auth BY]
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: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28EA [auth AZ],
JB [auth BZ]
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: 5
MoleculeChains LengthOrganismImage
16S rRNAF [auth AA],
KA [auth BA]
1,495Pyrococcus furiosus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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