8BGU

human MDM2-5S RNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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 30: 1119-1131

  • 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A [auth F]491Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5C [auth A]297Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
UniProt & NIH Common Fund Data Resources
Find proteins for P46777 (Homo sapiens)
Explore P46777 
Go to UniProtKB:  P46777
PHAROS:  P46777
GTEx:  ENSG00000122406 
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UniProt GroupP46777
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11D [auth B]178Homo sapiensMutation(s): 0 
Gene Names: RPL11
UniProt & NIH Common Fund Data Resources
Find proteins for P62913 (Homo sapiens)
Explore P62913 
Go to UniProtKB:  P62913
PHAROS:  P62913
GTEx:  ENSG00000142676 
Entity Groups  
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UniProt GroupP62913
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNAB [auth 3]121Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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)European Union885711

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references