8V9R

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Branched-Degron DHFR-ssrA Substrate Bound with MTX

Summary for 8V9R

• Entry DOI: 10.2210/pdb8v9r/pdb
• EMDB information: 43081
• Descriptor: ATP-dependent Clp protease ATP-binding subunit ClpX, Dihydrofolate reductase, ATP-dependent Clp protease proteolytic subunit, ... (7 entities in total)
• Functional Keywords: clpxp, full-engaged state, aaa protease, chaperone
• Biological source: Escherichia coli; More
• Total number of polymer chains: 21
• Total formula weight: 609712.45

Authors

Ghanbarpour, A.,Sauer, R.T.,Davis, J.H. (deposition date: 2023-12-09, release date: 2024-10-16, Last modification date: 2025-04-30)

Primary citation

Ghanbarpour, A.,Sauer, R.T.,Davis, J.H.
A proteolytic AAA+ machine poised to unfold protein substrates.
Nat Commun, 15:9681-9681, 2024

PubMed Abstract: AAA+ proteolytic machines unfold proteins before degrading them. Here, we present cryoEM structures of ClpXP-substrate complexes that reveal a postulated but heretofore unseen intermediate in substrate unfolding/degradation. A ClpX hexamer draws natively folded substrates tightly against its axial channel via interactions with a fused C-terminal degron tail and ClpX-RKH loops that flexibly conform to the globular substrate. The specific ClpX-substrate contacts observed vary depending on the substrate degron and affinity tags, helping to explain ClpXP's ability to unfold/degrade a wide array of different cellular substrates. Some ClpX contacts with native substrates are enabled by upward movement of the seam subunit in the AAA+ spiral, a motion coupled to a rearrangement of contacts between the ClpX unfoldase and ClpP peptidase. Our structures additionally highlight ClpX's ability to translocate a diverse array of substrate topologies, including the co-translocation of two polypeptide chains.

PubMed: 39516482
DOI: 10.1038/s41467-024-53681-9

Experimental method

ELECTRON MICROSCOPY (2.8 Å)