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Structure paper

TitleThe DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 3296, Year 2024
Publish dateApr 17, 2024
AuthorsVictor E Cruz / Christine S Weirich / Nagesh Peddada / Jan P Erzberger /
PubMed AbstractDEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this ...DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit.
External linksNat Commun / PubMed:38632236 / PubMed Central
MethodsEM (single particle)
Resolution2.47 - 3.58 Å
Structure data

43017

8v83

EMDB-43017, PDB-8v83:
60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
Method: EM (single particle) / Resolution: 2.53 Å

EMDB-43018: 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - PTC Local map)
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-43019: 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Local map L1 region)
Method: EM (single particle) / Resolution: 3.58 Å

EMDB-43020: 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Local map Rrp14/Rrp15/Ssf1 region)
Method: EM (single particle) / Resolution: 2.47 Å

43021

8v84

EMDB-43021, PDB-8v84:
60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-43022: 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Dbp10 Local map)
Method: EM (single particle) / Resolution: 2.9 Å

43023

8v85

EMDB-43023, PDB-8v85:
60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Low-pass filtered locally refined map)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-43024: 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - L1 local map
Method: EM (single particle) / Resolution: 3.57 Å

EMDB-43026: 60S ribosome biogenesis intermediate (Dbp10 catalytic intermediate - Rrp14/Rrp15/Ssf1 local map)
Method: EM (single particle) / Resolution: 2.81 Å

43027

8v87

EMDB-43027, PDB-8v87:
60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
Method: EM (single particle) / Resolution: 2.66 Å

EMDB-43028: 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Dbp10 Local map)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-43029: 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - H64 Local map)
Method: EM (single particle) / Resolution: 2.92 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

ChemComp-MG:
Unknown entry

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

ChemComp-K:
Unknown entry

Source
  • saccharomyces cerevisiae by4741 (yeast)
  • saccharomyces cerevisiae by4741-av16 (yeast)
KeywordsRIBOSOME / Ribosome biogenesis intermediate DEAD-box ATPase / Ribosome/RNA / Ribosome biogenesis / intermediate DEAD-box ATPase / Ribosome-RNA complex / RNA BINDING PROTEIN / RNA Binding

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