9FNY image
Entry Detail
PDB ID:
9FNY
EMDB ID:
Keywords:
Title:
PF30S-PF30S dimer mediated by aRDF from P. furiosus (Structure I)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-06-11
Release Date:
2025-01-15
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:RNA-binding protein
Chain IDs:A (auth: A1), FA (auth: B1)
Chain Length:60
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS32
Chain IDs:B (auth: A2), GA (auth: B2)
Chain Length:37
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Archaeal Ribosome Dimerizing Factor (aRDF)
Chain IDs:C (auth: A3), D (auth: A4), HA (auth: B3), IA (auth: B4)
Chain Length:306
Number of Molecules:4
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL8
Chain IDs:E (auth: A5), JA (auth: B5)
Chain Length:123
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:F (auth: AA), KA (auth: BA)
Chain Length:1495
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS2
Chain IDs:G (auth: AB), LA (auth: BB)
Chain Length:202
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS3
Chain IDs:H (auth: AC), MA (auth: BC)
Chain Length:210
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS1
Chain IDs:I (auth: AD), NA (auth: BD)
Chain Length:198
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS4
Chain IDs:J (auth: AE), OA (auth: BE)
Chain Length:180
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS4
Chain IDs:K (auth: AF), PA (auth: BF)
Chain Length:243
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS5
Chain IDs:L (auth: AG), QA (auth: BG)
Chain Length:236
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS6
Chain IDs:M (auth: AH), RA (auth: BH)
Chain Length:125
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS7
Chain IDs:N (auth: AI), SA (auth: BI)
Chain Length:215
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS8
Chain IDs:O (auth: AJ), TA (auth: BJ)
Chain Length:130
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS8
Chain IDs:P (auth: AK), UA (auth: BK)
Chain Length:127
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS9
Chain IDs:Q (auth: AL), VA (auth: BL)
Chain Length:135
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS10
Chain IDs:R (auth: AM), WA (auth: BM)
Chain Length:102
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS11
Chain IDs:S (auth: AN), XA (auth: BN)
Chain Length:137
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS12
Chain IDs:T (auth: AO), YA (auth: BO)
Chain Length:147
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS13
Chain IDs:U (auth: AP), ZA (auth: BP)
Chain Length:148
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS14
Chain IDs:V (auth: AQ), AB (auth: BQ)
Chain Length:56
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS15
Chain IDs:W (auth: AR), BB (auth: BR)
Chain Length:158
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS17
Chain IDs:X (auth: AS), CB (auth: BS)
Chain Length:113
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS17
Chain IDs:Y (auth: AT), DB (auth: BT)
Chain Length:67
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS19
Chain IDs:Z (auth: AU), EB (auth: BU)
Chain Length:132
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS19
Chain IDs:AA (auth: AV), FB (auth: BV)
Chain Length:150
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS24
Chain IDs:BA (auth: AW), GB (auth: BW)
Chain Length:99
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS31
Chain IDs:CA (auth: AX), HB (auth: BX)
Chain Length:50
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS27
Chain IDs:DA (auth: AY), IB (auth: BY)
Chain Length:63
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS28
Chain IDs:EA (auth: AZ), JB (auth: BZ)
Chain Length:71
Number of Molecules:2
Biological Source:Pyrococcus furiosus
Ligand Molecules
Primary Citation
Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization.
Nucleic Acids Res. 53 ? ? (2025)
PMID: 39797736 DOI: 10.1093/nar/gkae1324

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures