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Structure paper

TitleCommunication network within the essential AAA-ATPase Rix7 drives ribosome assembly.
Journal, issue, pagesPNAS Nexus, Vol. 1, Issue 4, Page pgac118, Year 2022
Publish dateJul 21, 2022
AuthorsSeda Kocaman / Yu-Hua Lo / Juno M Krahn / Mack Sobhany / Venkata P Dandey / Matthew L Petrovich / Suhas K Etigunta / Jason G Williams / Leesa J Deterding / Mario J Borgnia / Robin E Stanley /
PubMed AbstractRix7 is an essential AAA+ ATPase that functions during the early stages of ribosome biogenesis. Rix7 is composed of three domains including an N-terminal domain (NTD) and two AAA+ domains (D1 and ...Rix7 is an essential AAA+ ATPase that functions during the early stages of ribosome biogenesis. Rix7 is composed of three domains including an N-terminal domain (NTD) and two AAA+ domains (D1 and D2) that assemble into an asymmetric stacked hexamer. It was recently established that Rix7 is a presumed protein translocase that removes substrates from preribosomes by translocating them through its central pore. However, how the different domains of Rix7 coordinate their activities within the overall hexameric structure was unknown. We captured cryo-electron microscopy (EM) structures of single and double Walker B variants of full length Rix7. The disordered NTD was not visible in the cryo-EM reconstructions, but cross-linking mass spectrometry revealed that the NTD can associate with the central channel in vitro. Deletion of the disordered NTD enabled us to obtain a structure of the Rix7 hexamer to 2.9 Å resolution, providing high resolution details of critical motifs involved in substrate translocation and interdomain communication. This structure coupled with cell-based assays established that the linker connecting the D1 and D2 domains as well as the pore loops lining the central channel are essential for formation of the large ribosomal subunit. Together, our work shows that Rix7 utilizes a complex communication network to drive ribosome biogenesis.
External linksPNAS Nexus / PubMed:36090660 / PubMed Central
MethodsEM (single particle)
Resolution2.88 - 4.3 Å
Structure data

25474

7swl

EMDB-25474, PDB-7swl:
CryoEM structure of the N-terminal-deleted Rix7 AAA-ATPase
Method: EM (single particle) / Resolution: 2.88 Å

25582

7t0v

EMDB-25582, PDB-7t0v:
CryoEM structure of the crosslinked Rix7 AAA-ATPase
Method: EM (single particle) / Resolution: 3.67 Å

25659

7t3i

EMDB-25659, PDB-7t3i:
CryoEM structure of the Rix7 D2 Walker B mutant
Method: EM (single particle) / Resolution: 4.3 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-MG:
Unknown entry

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

ChemComp-PO4:
PHOSPHATE ION / Phosphate

Source
  • chaetomium thermophilum (fungus)
  • synthetic construct (others)
  • escherichia coli (E. coli)
KeywordsRIBOSOMAL PROTEIN / AAA-ATPase / ribosome biogenesis / substrate translocation / CryoEM / Rix7

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