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- PDB-9fo0: PF30S ribosomal subunit - control -

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Basic information

Entry
Database: PDB / ID: 9fo0
TitlePF30S ribosomal subunit - control
Components
  • (Small ribosomal subunit protein ...) x 26
  • 16S rRNA
  • Large ribosomal subunit protein eL8
  • RNA-binding protein
KeywordsTRANSLATION / Pyrococcus furiosus / ribosomal subunit / dimerization / anti-association / ribosome-associated protein
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea ...Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S27e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / RNA-binding protein / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / RNA-binding protein / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS27
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHassan, A.H. / Demo, G.
Funding support Czech Republic, European Union, 2items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLL2008 Czech Republic
European Union (EU)LX22NPO5103European Union
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization.
Authors: Ahmed H Hassan / Matyas Pinkas / Chiaki Yaeshima / Sonoko Ishino / Toshio Uchiumi / Kosuke Ito / Gabriel Demo /
Abstract: Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often ...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.
History
DepositionJun 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: RNA-binding protein
A2: Small ribosomal subunit protein eS32
A5: Large ribosomal subunit protein eL8
AA: 16S rRNA
AB: Small ribosomal subunit protein uS2
AC: Small ribosomal subunit protein uS3
AD: Small ribosomal subunit protein eS1
AE: Small ribosomal subunit protein uS4
AF: Small ribosomal subunit protein eS4
AG: Small ribosomal subunit protein uS5
AH: Small ribosomal subunit protein eS6
AI: Small ribosomal subunit protein uS7
AJ: Small ribosomal subunit protein uS8
AK: Small ribosomal subunit protein eS8
AL: Small ribosomal subunit protein uS9
AM: Small ribosomal subunit protein uS10
AN: Small ribosomal subunit protein uS11
AO: Small ribosomal subunit protein uS12
AP: Small ribosomal subunit protein uS13
AQ: Small ribosomal subunit protein uS14
AR: Small ribosomal subunit protein uS15
AS: Small ribosomal subunit protein uS17
AT: Small ribosomal subunit protein eS17
AU: Small ribosomal subunit protein uS19
AV: Small ribosomal subunit protein eS19
AW: Small ribosomal subunit protein eS24
AX: Small ribosomal subunit protein eS31
AY: Small ribosomal subunit protein eS27
AZ: Small ribosomal subunit protein eS28


Theoretical massNumber of molelcules
Total (without water)911,16229
Polymers911,16229
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules A1A5

#1: Protein RNA-binding protein


Mass: 6824.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: A0A5C0XRZ8
#3: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13414.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U160

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Small ribosomal subunit protein ... , 26 types, 26 molecules A2ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZ

#2: Protein/peptide Small ribosomal subunit protein eS32 / 50S ribosomal protein L41e / Large ribosomal subunit protein eL41


Mass: 5023.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U232
#5: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 23039.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0F0
#6: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 23464.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U004
#7: Protein Small ribosomal subunit protein eS1 / 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 22984.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZE1
#8: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 21381.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P61993
#9: Protein Small ribosomal subunit protein eS4 / 30S ribosomal protein S4e


Mass: 28197.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U011
#10: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5 / PfS5


Mass: 26590.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U017
#11: Protein Small ribosomal subunit protein eS6 / 30S ribosomal protein S6e


Mass: 14002.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U3H8
#12: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 24701.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0M8
#13: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14684.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U014
#14: Protein Small ribosomal subunit protein eS8 / 30S ribosomal protein S8e


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U1Y5
#15: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 15317.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E7
#16: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11769.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P61885
#17: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14756.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E3
#18: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 16477.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P61995
#19: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 16948.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E2
#20: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14 type Z


Mass: 6634.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U013
#21: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 18640.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZD9
#22: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 13296.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U008
#23: Protein Small ribosomal subunit protein eS17 / 30S ribosomal protein S17e


Mass: 7942.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0U1
#24: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 15357.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U002
#25: Protein Small ribosomal subunit protein eS19


Mass: 17394.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0T4
#26: Protein Small ribosomal subunit protein eS24 / 30S ribosomal protein S24e


Mass: 11698.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U442
#27: Protein/peptide Small ribosomal subunit protein eS31 / 30S ribosomal protein S27ae


Mass: 5864.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U443
#28: Protein Small ribosomal subunit protein eS27 / 30S ribosomal protein S27e


Mass: 6888.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U474
#29: Protein Small ribosomal subunit protein eS28 / 30S ribosomal protein S28e


Mass: 8116.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U159

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RNA chain , 1 types, 1 molecules AA

#4: RNA chain 16S rRNA


Mass: 485455.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PF30S control / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.85 MDa / Experimental value: NO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES-KOHHEPES-KOH1
212 mMmagnesium chlorideMgCl21
3100 mMamonium chlorideNH4Cl1
40.5 mMEDTAEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277.6 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6697

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Processing

EM software
IDNameVersionCategory
1cisTEM1.1.0particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10FREALIGN9.11initial Euler assignment
11FREALIGN9.11final Euler assignment
12FREALIGN9.11classification
13FREALIGN9.113D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 274032
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25356 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14V6U

4v6u

14V6U1PDBexperimental model
27ZHG

7zhg

17ZHG2PDBexperimental model
31ITasserin silico model

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