8OOI

Full composite cryo-EM map of p97/VCP in ADP.Pi state

Summary for 8OOI

• Entry DOI: 10.2210/pdb8ooi/pdb
• EMDB information: 16781 16782 17016 17128
• Descriptor: Transitional endoplasmic reticulum ATPase, ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, ... (7 entities in total)
• Functional Keywords: aaa+ atpase, complex, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 6
• Total formula weight: 543323.29

Authors

Cheng, T.C.,Sakata, E.,Schuetz, A.K. (deposition date: 2023-04-05, release date: 2024-01-31, Last modification date: 2024-10-16)

Primary citation

Shein, M.,Hitzenberger, M.,Cheng, T.C.,Rout, S.R.,Leitl, K.D.,Sato, Y.,Zacharias, M.,Sakata, E.,Schutz, A.K.
Characterizing ATP processing by the AAA+ protein p97 at the atomic level.
Nat.Chem., 16:363-372, 2024

PubMed Abstract: The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·P state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.

PubMed: 38326645
DOI: 10.1038/s41557-024-01440-0

Experimental method

ELECTRON MICROSCOPY (2.61 Å)