5WVK

Yeast proteasome-ADP-AlFx

This is a non-PDB format compatible entry.

Summary for 5WVK

• Entry DOI: 10.2210/pdb5wvk/pdb
• EMDB information: 6694
• Descriptor: Proteasome subunit beta type-1, Proteasome subunit alpha type-3, Proteasome subunit alpha type-4, ... (33 entities in total)
• Functional Keywords: transition state mimic, yeast proteasome, high resolution, asymmetric nucleotide occupancy, hydrolase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 47
• Total formula weight: 1692659.85

Authors

Ding, Z.,Cong, Y. (deposition date: 2016-12-25, release date: 2017-03-22, Last modification date: 2024-03-27)

Primary citation

Ding, Z.,Fu, Z.,Xu, C.,Wang, Y.,Wang, Y.,Li, J.,Kong, L.,Chen, J.,Li, N.,Zhang, R.,Cong, Y.
High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx
Cell Res., 27:373-385, 2017

PubMed Abstract: The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by the proteasome.

PubMed: 28106073
DOI: 10.1038/cr.2017.12

Experimental method

ELECTRON MICROSCOPY (4.2 Å)