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TitleSubstrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding.
Journal, issue, pagesScience, Vol. 365, Issue 6452, Year 2019
Publish dateAug 2, 2019
AuthorsEdward C Twomey / Zhejian Ji / Thomas E Wales / Nicholas O Bodnar / Scott B Ficarro / Jarrod A Marto / John R Engen / Tom A Rapoport /
PubMed AbstractThe Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for ...The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-electron microscopy structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and polyubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates.
External linksScience / PubMed:31249135 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 4.1 Å
Structure data

0665

6oa9

EMDB-0665: Cdc48-Ufd1/Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
PDB-6oa9: Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Method: EM (single particle) / Resolution: 3.9 Å

0666

6oaa

EMDB-0666: Cdc48-Ufd1/Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1
PDB-6oaa: Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1
Method: EM (single particle) / Resolution: 4.1 Å

20000

6oab

EMDB-20000: Cdc48-Ufd1/Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2
PDB-6oab: Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

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

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

ChemComp-ZN:
Unknown entry

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsMOTOR PROTEIN / ATPase / ATPase complex / ubiquitin / quality control

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