7OZS

Structure of the hexameric 5S RNP from C. thermophilum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways.

Castillo Duque de Estrada, N.M.Thoms, M.Flemming, D.Hammaren, H.M.Buschauer, R.Ameismeier, M.Bassler, J.Beck, M.Beckmann, R.Hurt, E.

(2023) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-023-01006-7
  • Primary Citation of Related Structures:  
    7OZS, 8BGU

  • PubMed 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 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.


  • Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinA [auth B]173Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SHQ2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0SHQ2
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UniProt GroupG0SHQ2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l5-like proteinB [auth A]304Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SEG2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0SEG2
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UniProt GroupG0SEG2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis regulatory proteinC [auth D]202Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SCH6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SCH6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome production factor 2 homologD [auth C]350Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SF80 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SF80
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
unknownF [auth E]23Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Syo1G [auth F]676Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S5S6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S5S6 
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S rRNAE [auth 3]119Thermochaetoides thermophila DSM 1495
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRK1721
German Research Foundation (DFG)GermanyHU363/15-2
European Research Council (ERC)Germany885711

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-06-21
    Changes: Database references