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- PDB-7ozs: Structure of the hexameric 5S RNP from C. thermophilum -

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Basic information

Entry
Database: PDB / ID: 7ozs
TitleStructure of the hexameric 5S RNP from C. thermophilum
Components
  • 5S rRNA
  • 60S ribosomal protein l5-like protein
  • Putative ribosomal protein
  • Ribosome biogenesis regulatory protein
  • Ribosome production factor 2 homolog
  • Syo1
  • unknown
KeywordsRNA BINDING PROTEIN / 5S RNP / Ribosome biogenesis / Symportin 1 / Rpf2-Rrs1
Function / homology
Function and homology information


ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein import into nucleus / unfolded protein binding / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome ...ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein import into nucleus / unfolded protein binding / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / nucleolus / nucleus
Similarity search - Function
: / Ribosome biogenesis protein Rpf2 / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Nucleotidyltransferase; domain 5 - #100 / Brix domain / Brix domain / Brix domain profile. / Brix / Ribosomal protein L5 eukaryotic, C-terminal ...: / Ribosome biogenesis protein Rpf2 / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Nucleotidyltransferase; domain 5 - #100 / Brix domain / Brix domain / Brix domain profile. / Brix / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Armadillo-like helical / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Nucleotidyltransferase; domain 5 / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Symportin 1 / Ribosome biogenesis regulatory protein homolog / Large ribosomal subunit protein uL18 / Ribosome production factor 2 homolog / Large ribosomal subunit protein uL5
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Chaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCastillo, N. / Thoms, M. / Flemming, D. / Hammaren, H.M. / Buschauer, R. / Ameismeier, M. / Bassler, J. / Beck, M. / Beckmann, R. / Hurt, E.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)RK1721 Germany
German Research Foundation (DFG)HU363/15-2 Germany
European Research Council (ERC)885711 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways.
Authors: Nestor Miguel Castillo Duque de Estrada / Matthias Thoms / Dirk Flemming / Henrik M Hammaren / Robert Buschauer / Michael Ameismeier / Jochen Baßler / Martin Beck / Roland Beckmann / Ed Hurt /
Abstract: The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is ...The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is disturbed, a free 5S RNP can enter the MDM2-p53 pathway to regulate cell cycle and apoptotic signaling. Here we reconstitute and determine the cryo-electron microscopy structure of the conserved hexameric 5S RNP with fungal or human factors. This reveals how the nascent 5S rRNA associates with the initial nuclear import complex Syo1-uL18-uL5 and, upon further recruitment of the nucleolar factors Rpf2 and Rrs1, develops into the 5S RNP precursor that can assemble into the pre-ribosome. In addition, we elucidate the structure of another 5S RNP intermediate, carrying the human ubiquitin ligase Mdm2, which unravels how this enzyme can be sequestered from its target substrate p53. Our data provide molecular insight into how the 5S RNP can mediate between ribosome biogenesis and cell proliferation.
History
DepositionJun 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative ribosomal protein
A: 60S ribosomal protein l5-like protein
D: Ribosome biogenesis regulatory protein
C: Ribosome production factor 2 homolog
3: 5S rRNA
E: unknown
F: Syo1


Theoretical massNumber of molelcules
Total (without water)232,8967
Polymers232,8967
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, immunoprecipitation, cross-linking, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules BADCF

#1: Protein Putative ribosomal protein


Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ2
#2: Protein 60S ribosomal protein l5-like protein


Mass: 35034.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEG2
#3: Protein Ribosome biogenesis regulatory protein


Mass: 22817.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCH6
#4: Protein Ribosome production factor 2 homolog / Ribosome biogenesis protein RPF2 homolog


Mass: 39927.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SF80
#7: Protein Syo1


Mass: 74709.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5S6

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RNA chain / Protein/peptide , 2 types, 2 molecules 3E

#5: RNA chain 5S rRNA


Mass: 38312.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
#6: Protein/peptide unknown


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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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: hexameric 5S RNP from C. thermophilum / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 43.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126547 / Symmetry type: POINT

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