Structural basis of ubiquitin‐independent PP1 complex disassembly by p97

Abstract

The AAA+‐ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is unclear. Here, we present cryo‐EM structures of p97 in the process of disassembling a protein phosphatase‐1 (PP1) complex by extracting an inhibitory subunit from PP1. We show that PP1 and its partners SDS22 and inhibitor‐3 (I3) are loaded tightly onto p97, surprisingly via a direct contact of SDS22 with the p97 N‐domain. Loading is assisted by the p37 adapter that bridges two adjacent p97 N‐domains underneath the substrate complex. A stretch of I3 is threaded into the central channel of the spiral‐shaped p97 hexamer, while other elements of I3 are still attached to PP1. Thus, our data show how p97 arranges a protein complex between the p97 N‐domain and central channel, suggesting a hold‐and‐extract mechanism for p97‐mediated disassembly. image It remains unclear how substrate complexes are loaded onto the p97/VCP AAA+‐ATPase and disassembled. Here, structures show p97 bound to a PP1‐regulatory complex undergoing disassembly and suggest a hold‐and‐extract mechanism. Cryo‐EM shows p97 and its p37 adapter loaded with a ternary PP1 complex as a substrate for disassembly. The PP1 partner SDS22 is bound tightly and directly to an N‐domain of p97. The I3 partner of PP1 is inserted into the central channel of p97 while still attached to PP1. p97 is in an active staircase conformation primed to strip the I3 subunit off PP1.