Hello everyone

We are building an atomic structure model against a cryo-EM map of AAA+ ATPase.

Considering that AAA+ polymerizes when ATP is added, we collected data for AAA+ mixed with ATP. Our AAA+ ATPase protein contains every conserved residue needed for the hydrolysis of ATP into ADP and Pi.

Now while building the model, i noticed an empty density blob where ADP fits well, however, ATP is too bulky for it.

Has anyone seen any literature or experienced a similar situation where the protein supplemented with ATP but ADP is observed in the crystal or cryo-EM structure?

I have also attached images showing the fitted ADP molecule and its cryo-EM density, for your perusal.

Any suggestions will be greatly appreciated.

Thanks.

Ketul