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Structure paper

TitleMechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
Journal, issue, pagesEMBO Rep, Vol. 24, Issue 7, Page e56910, Year 2023
Publish dateJul 5, 2023
AuthorsBenjamin Lau / Zixuan Huang / Nikola Kellner / Shuangshuang Niu / Otto Berninghausen / Roland Beckmann / Ed Hurt / Jingdong Cheng /
PubMed AbstractRibosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ...Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.
External linksEMBO Rep / PubMed:37129998 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.6 Å
Structure data

EMDB-35279, PDB-8i9p:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-35281, PDB-8i9r:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-35283, PDB-8i9t:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-35285, PDB-8i9v:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-35286, PDB-8i9w:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-35287, PDB-8i9x:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-35288, PDB-8i9y:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-35289, PDB-8i9z:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-35290, PDB-8ia0:
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6
Method: EM (single particle) / Resolution: 2.7 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • chaetomium thermophilum (fungus)
KeywordsRIBOSOME / Ribosome biogenesis / pre-60S ribosome

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