Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4

Many poly-ubiquitinated proteins are extracted from membranes or complexes by a conserved ATPase, called Cdc48 in yeast and p97/VCP in mammals, before proteasomal degradation(1). Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains(2). Cdc48 binds various cofactors, including a heterodimer of Ufd1 and Npl4(3). Here, we report structures of the Cdc48-Ufd1-Npl4 ATPase complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and uses two Zn(2+)-finger domains to anchor an enzymatically inactive Mpr1/Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48’s central pore, similarly to the MPN of the de-ubiquitinase Rpn11 in the proteasome(4). Our results indicate that Npl4 is unique among Cdc48 cofactors, and suggest a mechanism for how poly-ubiquitinated substrates bind to and translocate into the ATPase.