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Structure paper

TitleVisualization of the Cdc48 AAA+ ATPase protein unfolding pathway.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 7505, Year 2024
Publish dateAug 29, 2024
AuthorsIan Cooney / Heidi L Schubert / Karina Cedeno / Olivia N Fisher / Richard Carson / John C Price / Christopher P Hill / Peter S Shen /
PubMed AbstractThe Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, ...The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of native structures of Cdc48 affinity purified from budding yeast lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data uncover elements of Shp1-Cdc48 interactions and support a 'hand-over-hand' mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by the D2 motor in substrate translocation/unfolding.
External linksNat Commun / PubMed:39209885 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 4.3 Å
Structure data

41992

8u7t

EMDB-41992, PDB-8u7t:
Substrate-bound Cdc48, Class 1
Method: EM (single particle) / Resolution: 3.3 Å

42025

8u8i

EMDB-42025, PDB-8u8i:
Cdc48-Shp1 unfolding native substrate, Class 4
Method: EM (single particle) / Resolution: 3.5 Å

42032

8u9c

EMDB-42032, PDB-8u9c:
Cdc48-Shp1 unfolding native substrate, Class 5
Method: EM (single particle) / Resolution: 3.7 Å

42038

8u9p

EMDB-42038, PDB-8u9p:
Cdc48-Shp1 unfolding native substrate, Class 2
Method: EM (single particle) / Resolution: 3.2 Å

42039

8u9q

EMDB-42039, PDB-8u9q:
Cdc48-Shp1 unfolding native substrate, Class 6
Method: EM (single particle) / Resolution: 4.3 Å

42042

8u9z

EMDB-42042, PDB-8u9z:
Cdc48-Shp1 unfolding native substrate, Class 7
Method: EM (single particle) / Resolution: 3.8 Å

42043

8ua0

EMDB-42043, PDB-8ua0:
Cdc48-Shp1 unfolding native substrate, Class 8
Method: EM (single particle) / Resolution: 3.5 Å

42047

8ua1

EMDB-42047, PDB-8ua1:
Cdc48-Shp1 unfolding native substrate, Class 9
Method: EM (single particle) / Resolution: 3.4 Å

42057

8uaa

EMDB-42057, PDB-8uaa:
Cdc48-Shp1 unfolding native substrate, Class 3
Method: EM (single particle) / Resolution: 3.4 Å

42076

8ub4

EMDB-42076, PDB-8ub4:
Cdc48-Shp1 unfolding native substrate, consensus structure
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-08T:
[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium

ChemComp-MG:
Unknown entry

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

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsCHAPERONE / unfoldase / AAA ATPase / p97 / Cdc48

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