p97(also known as Cdc48 or VCP) is a conserved AAA+ ATPase that plays a key role in diverse cellular pathways and processes. p97 segregates damaged or misfolded substrates from cellular organelles or membranes in corporation with its cofactors. SAKS1 is one of the important cofactors of p97 because this protein in contrast to the other cofactors has an inhibitory effect of p97 activity. This cofactor binds ubiquitin molecule and p97 through its UBA and UBX domain, respectively. SAKS1 regulates ERAD activity only in association with both polyubiquitin and p97, indicating its effect is based on the presence of both factors. However, the mechanism of substrate processing via human p97 ATPase in combination with SAKS1 remains poorly understood. Therefore, we aimed to study protein-protein interaction between p97 and SAKS1 and determine determine the high-resolution structure of p97 in complex with cofactor and generated substrate to provide structural insights into the molecular mechanism of substrate-processing by p97.