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The Proteasome Structure

The Proteasome Structure

The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
The proteasome is an...

The Proteasome

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...

The Proteasome

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...

The Proteasome

The Proteasome

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Mechanical Protein Functions

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.

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Related Experiment Video

Updated: Nov 28, 2025

Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach

Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach

Published on: December 17, 2016

Structure, Dynamics and Function of the 26S Proteasome.

Youdong Mao^1,2

¹Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. youdong_mao@dfci.harvard.edu.

Sub-Cellular Biochemistry

|November 30, 2020

Summary

The 26S proteasome, a large cellular machine, degrades proteins. New cryo-EM studies reveal its atomic-level dynamics, uncovering how it engages, deubiquitylates, and degrades protein substrates.

Keywords:

AAA-ATPase motor Conformational dynamics Cryo-EM Cryogenic electron microscopy Deubiquitylation Homeostasis Mechanochemistry Proteasome Proteolysis Ubiquitin-proteasome system Ubiquitylation

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Last Updated: Nov 28, 2025

Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach

Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach

Published on: December 17, 2016

Quantifying Subcellular Ubiquitin-proteasome Activity in the Rodent Brain

Quantifying Subcellular Ubiquitin-proteasome Activity in the Rodent Brain

Published on: May 21, 2019

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

The 26S proteasome is a large, ATP-dependent protease complex essential for eukaryotic cellular function.
It degrades ubiquitinated proteins, regulating diverse cellular processes.
Its complex mechanism has remained enigmatic despite its importance.

Purpose of the Study:

To elucidate the atomic-level mechanisms of the 26S proteasome during substrate degradation.
To understand substrate engagement, deubiquitylation, and translocation processes.
To reveal the role of AAA-ATPase activity in proteasome function.

Main Methods:

Cryogenic electron microscopy (cryo-EM) for high-resolution 3D visualization.
Analysis of proteasome dynamics during polyubiquitylated substrate degradation.
Structural studies of key protein-protein interactions and conformational changes.

Main Results:

Detailed visualization of ubiquitin binding and substrate engagement.
Insights into RPN11 deubiquitylating activity coupled with substrate translocation.
Discovery of three distinct modes of ATP hydrolysis regulating proteasome function.
Atomic-level understanding of substrate processing and degradation initiation.

Conclusions:

Cryo-EM has provided unprecedented atomic detail of 26S proteasome function.
Understanding these mechanisms offers new insights into the ubiquitin-proteasome system.
These findings have significant implications for cellular regulation, health, and disease.