Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry.

Nicole S MacRae, Ken C Dong, Hiromitsu Harimoto, Andreas Martin

Abstract read

In one paragraph

Article in The Journal of biological chemistry, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

Mapping Interaction of Assembly Factor Rpn14 With the Proteasome Base Reveals a Bipartite Interface and Implies Ordered Remodeling of Intersubunit Contacts During Proteasome Biogenesis.Journal of molecular biology · 2026
Article

4 · The record

Corrections and comments

Update of
Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry.2025

5 · Who and what money

Authors and funding

4 authors.

Nicole S MacRaeDepartment of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California, USA; Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, USA.

Ken C DongHoward Hughes Medical Institute, University of California at Berkeley, Berkeley, California, USA.

Hiromitsu HarimotoDepartment of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA.

Andreas MartinDepartment of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California, USA. Electronic address: a.martin@berkeley.edu.

Funding

ATP-Dependent Protein Unfolding and Translocation by the Eukaryotic ProteasomeR01GM094497 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI MARTIN, ANDREAS · 2011 to 2024

$3.7M

Biophysics Training ProgramT32GM146614 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI James H Hurley, Ahmet Yildiz · 2023 to 2026

$2.5M

NIGMS NIH HHS R01 GM094497NIGMS NIH HHS T32 GM146614

6 · The paper itself

Abstract

The 26S proteasome is the endpoint of the ubiquitin-proteasome system, an essential pathway for maintaining cellular homeostasis through targeted degradation of misfolded, damaged, and obsolete proteins. Substrates labeled with ubiquitin are directed to the 26S proteasome by binding to one or more ubiquitin receptors. However, ubiquitin-dependent degradation occurs even when the canonical receptor sites are mutated, suggesting the presence of additional, unidentified binding sites. Here we created photo-crosslinkable probes for ubiquitin interactions by incorporating the unnatural amino acid p-benzoyl-L-phenylalanine into ubiquitin. We show that these probes can be used to measure apparent affinities for known receptors and to reveal novel ubiquitin-binding sites on the yeast 26S proteasome. Through photo-crosslinking mass-spectrometry experiments, we identified a groove on the top of the proteasome, formed by Rpn2, Rpn9, Rpn10, and Rpn12, that serves as an additional tubiquitin-binding interface. Our photo-crosslinkable probes thus serve as versatile tools for the characterization of ubiquitin-protein interactions and the identification of ubiquitin-binding domains.

Indexed as

Cross-Linking ReagentsProteasome Endopeptidase ComplexSaccharomyces cerevisiae ProteinsUbiquitinBenzophenonesBinding SitesMass SpectrometryPhenylalaninePhotochemical ProcessesSaccharomyces cerevisiae4-benzoylphenylalanineATP dependent 26S proteaseBenzophenonesCross-Linking ReagentsPhenylalanineProteasome Endopeptidase ComplexSaccharomyces cerevisiae ProteinsUbiquitinATPases associated with diverse cellular activities (AAA)proteasomeprotein degradationproteostasisubiquitin

Identifiers

PMID42031168

DOI10.1016/j.jbc.2026.111481

PMCPMC13208731

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.