Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding

Science. 2019 Aug 2;365(6452):eaax1033. doi: 10.1126/science.aax1033. Epub 2019 Jun 27.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cryoelectron Microscopy
  • Multienzyme Complexes / chemistry*
  • Nucleocytoplasmic Transport Proteins / chemistry*
  • Polyubiquitin / chemistry*
  • Protein Domains
  • Protein Unfolding*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Substrate Specificity
  • Ubiquitination
  • Valosin Containing Protein / chemistry*
  • Valosin Containing Protein / genetics
  • Vesicular Transport Proteins / chemistry*


  • Multienzyme Complexes
  • NPL4 protein, S cerevisiae
  • Nucleocytoplasmic Transport Proteins
  • Saccharomyces cerevisiae Proteins
  • UFD1 protein, S cerevisiae
  • Vesicular Transport Proteins
  • Polyubiquitin
  • CDC48 protein, S cerevisiae
  • Valosin Containing Protein