Mechanisms of substrate recognition by the 26S proteasome

The ubiquitin code

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A 26 S protease subunit that binds ubiquitin conjugates.

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Proteasome subunit Rpn13 is a novel ubiquitin receptor

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Proteasome subunit Rpn1 binds ubiquitin-like protein domains

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Enhanced Protein Degradation by Branched Ubiquitin Chains

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An unstructured initiation site is required for efficient proteasome-mediated degradation

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Multiubiquitin Chain Receptors Define a Layer of Substrate Selectivity in the Ubiquitin-Proteasome System

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In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment

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Mechanism of Gate Opening in the 20S Proteasome by the Proteasomal ATPases

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Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction

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Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome

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A molecular census of 26 S proteasomes in intact neurons

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Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome

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Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding

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K63 ubiquitylation triggers proteasomal degradation by seeding branched ubiquitin chains

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Substrate-engaged 26 S proteasome structures reveal mechanisms for ATP-hydrolysis–driven translocation

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Lysine 63‐linked polyubiquitin chain may serve as a targeting signal for the 26S proteasome

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Conformational switching of the 26S proteasome enables substrate degradation

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Ubiquitin-independent proteasomal degradation

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Intrinsically Disordered Segments Affect Protein Half-Life in the Cell and during Evolution

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Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

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Defining the geometry of the two-component proteasome degron

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Structural basis for dynamic regulation of the human 26S proteasome

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Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination

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Proteasomes tether to two distinct sites at the nuclear pore complex

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The proteasome 19S cap and its ubiquitin receptors provide a versatile recognition platform for substrates

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Structure of the Rpn11–Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation

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Structural insights into the functional cycle of the ATPase module of the 26S proteasome

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APC/C-mediated multiple monoubiquitylation provides an alternative degradation signal for cyclin B1

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Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13

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The 26S Proteasome Utilizes a Kinetic Gateway to Prioritize Substrate Degradation

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Sequence composition of disordered regions fine-tunes protein half-life

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Proteasome substrate degradation requires association plus extended peptide

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The Cdc48 unfoldase prepares well-folded protein substrates for degradation by the 26S proteasome

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Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating

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Ufd2p synthesizes branched ubiquitin chains to promote the degradation of substrates modified with atypical chains

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Localization of the proteasomal ubiquitin receptors Rpn10 and Rpn13 by electron cryomicroscopy

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An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome

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Regulation of Proteasome Activity by (Post-)transcriptional Mechanisms

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Rad23 escapes degradation because it lacks a proteasome initiation region

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The Proteasome Distinguishes between Heterotypic and Homotypic Lysine-11-Linked Polyubiquitin Chains

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Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding

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Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome

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Proteins containing ubiquitin-like (Ubl) domains not only bind to 26S proteasomes but also induce their activation

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Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1

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Ubiquitin‐like domains can target to the proteasome but proteolysis requires a disordered region

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Origin and Functional Evolution of the Cdc48/p97/VCP AAA+ Protein Unfolding and Remodeling Machine

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Structure of Rpn10 and Its Interactions with Polyubiquitin Chains and the Proteasome Subunit Rpn12*

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Diverse fate of ubiquitin chain moieties: The proximal is degraded with the target, and the distal protects the proximal from removal and recycles

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Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome

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Intrinsic Disorder in Ubiquitination Substrates

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Sequence- and Species-Dependence of Proteasomal Processivity

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Site-specific ubiquitination affects protein energetics and proteasomal degradation

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Structure of hRpn10 Bound to UBQLN2 UBL Illustrates Basis for Complementarity between Shuttle Factors and Substrates at the Proteasome

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A masked initiation region in retinoblastoma protein regulates its proteasomal degradation

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Substrate selection by the proteasome through initiation regions

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Specific lid-base contacts in the 26s proteasome control the conformational switching required for substrate degradation

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An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure

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Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at hRpn11 of the 26S Proteasome

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Design principles that protect the proteasome from self‐destruction

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Design principles that protect the proteasome from self-destructionPreprint

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PROTAC targeted protein degraders: the past is prologue

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An expanded lexicon for the ubiquitin code

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Proteasome in action: substrate degradation by the 26S proteasome

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Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies

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Structural Insights into Substrate Recognition and Processing by the 20S Proteasome

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Intracellular localization of the proteasome in response to stress conditions

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Exploring the Role of Ubiquitin–Proteasome System in Parkinson's Disease

Behl, T., Kumar, S., Althafar, Z. M., Sehgal, A., Singh, S., Sharma, N., Badavath, V. N., Yadav, S., Bhatia, S., Al‐Harrasi, A., et al. (2022) · Molecular Neurobiology · doi:10.1007/s12035-022-02851-1 · Cited by 61 · see citing works

PA28γ: New Insights on an Ancient Proteasome Activator

Cascio, P. (2021) · Biomolecules · doi:10.3390/biom11020228 · Cited by 59 · see citing works

Allosteric control of Ubp6 and the proteasome via a bidirectional switch

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PROTAC: targeted drug strategy. Principles and limitations

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The E3 Ligase GmPUB21 Negatively Regulates Drought and Salinity Stress Response in Soybean

Yang, Y., Karthikeyan, A., Yin, J., Jin, T., Ren, R., Fang, F., Cai, H., Liu, M., Wang, D., Li, K., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23136893 · Cited by 35 · see citing works

The deubiquitinating enzyme STAMBP is a newly discovered driver of triple-negative breast cancer progression that maintains RAI14 protein stability

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The moonlighting of RAD23 in DNA repair and protein degradation

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Small-Molecule Inhibitors Targeting Proteasome-Associated Deubiquitinases

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Bortezomib advanced mechanisms of action in multiple myeloma, solid and liquid tumors along with its novel therapeutic applications

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Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation

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Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation

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Inhibition of HMGB1 Suppresses Hepatocellular Carcinoma Progression via HIPK2-Mediated Autophagic Degradation of ZEB1

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Fungal Secondary Metabolites as Inhibitors of the Ubiquitin–Proteasome System

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Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex

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Ubiquitin‐Independent Degradation: An Emerging PROTAC Approach?

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FtsH degrades dihydrofolate reductase by recognizing a partially folded species

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Stability of 20S Proteasome Configurations: Preopening the Axial Gate

Henderson, L. W., Sharon, E. M., Gautam, A. K. S., Anthony, A. J., Jarrold, M. F., Russell, D. H., Matouschek, A. T., & Clemmer, D. E. (2023) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.3c01040 · Cited by 10 · see citing works

The prognostic value of 19S ATPase proteasome subunits in acute myeloid leukemia and other forms of cancer

Tychhon, B., Allen, J. C., Gonzalez, M. A., Olivas, I. M., Solecki, J. P., Keivan, M., Velazquez, V. V., McCall, E. B., Tapia, D. N., Rubio, A. J., et al. (2023) · Frontiers in Medicine · doi:10.3389/fmed.2023.1209425 · Cited by 10 · see citing works

Primed for Interactions: Investigating the Primed Substrate Channel of the Proteasome for Improved Molecular Engagement

Loy, C. A., & Trader, D. J. (2024) · Molecules · doi:10.3390/molecules29143356 · Cited by 10 · see citing works

Recent advances in chemical proteomics for protein profiling and targeted degradation

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Advances in the study of protein folding and endoplasmic reticulum-associated degradation in mammal cells

Cao, H., Zhou, X., Xu, B., Hu, H., Guo, J., Ma, Y., Wang, M., Li, N., & Zou, J. (2024) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b2300403 · Cited by 9 · see citing works

CDMS Analysis of Intact 19S, 20S, 26S, and 30S Proteasomes: Evidence for Higher-Order 20S Assemblies at a Low pH

Anthony, A. J., Gautam, A. K. S., Miller, L. M., Ma, Y., Hardwick, A. G., Sharma, A., Ghatak, S., Matouschek, A. T., Jarrold, M. F., & Clemmer, D. E. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c00472 · Cited by 8 · see citing works

PROTAC technology for prostate cancer treatment

Wang, Z., Zhang, D., Inuzuka, H., & Wei, W. (2025) · Acta Materia Medica · doi:10.15212/amm-2024-0075 · Cited by 9 · see citing works

PSMC2 promotes glioma progression by regulating immune microenvironment and PI3K/AKT/mTOR pathway

Wang, Y., Zhang, S., Zhao, Z., Jin, Q., Wang, Z., Song, Z., Liu, L., & Zhao, Z. (2024) · Immunobiology · doi:10.1016/j.imbio.2024.152802 · Cited by 7 · see citing works

Insect antiviral Mx-like protein forms biomolecular condensates to promote viral capsid ubiquitinated degradation

Du, Y., Li, Y., Xiao, Y., Jia, D., & Wèi, T. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116146 · Cited by 7 · see citing works

Insight into Bortezomib Focusing on Its Efficacy against P-gp-Positive MDR Leukemia Cells

Kyca, T., Pavlíková, L., Boháčová, V., Mišák, A., Poturnayová, A., Breier, A., Sulová, Z., & Šereš, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115504 · Cited by 6 · see citing works

Evaluation of a Pooling Chemoproteomics Strategy with an FDA-Approved Drug Library

Sun, H., Yang, K., Zhang, X., Fu, Y., Yarbro, J. M., Wu, Z., Chen, P., Chen, T., & Peng, J. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00256 · Cited by 5 · see citing works

Proteasome subunit PSMD1 is a key therapeutic target in multiple myeloma

Du, T., Fang, T., Pillai, S. C., Ray, A., Wang, M., Wan, X., Wen, K., Liu, Y., Xu, J., Musa, M. A., et al. (2026) · Blood · doi:10.1182/blood.2025029358 · Cited by 5 · see citing works

The MUC5B promoter variant results in proteomic changes in the nonfibrotic lung

Herrera, J., Maslanka, M. D., Blumhagen, R. Z., Blomberg, R., Lwin, N. Y., Brancato, J., Cool, C. D., Huber, J. P., Kurche, J. S., Magin, C. M., et al. (2025) · JCI Insight · doi:10.1172/jci.insight.189636 · Cited by 4 · see citing works

p.Phe508del-CFTR Trafficking: A Protein Quality Control Perspective Through UPR, UPS, and Autophagy

Trouvé, P., & Férec, C. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26083623 · Cited by 4 · see citing works

The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence

Boussardon, C., Bag, P., Juvany, M., Šimura, J., Ljung, K., Jansson, S., & Keech, O. (2022) · Communications Biology · doi:10.1038/s42003-022-03998-2 · Cited by 4 · see citing works

Identification of the U-box gene family in peach (Prunus persica) and functional analysis of PpPUB20 in response to salt stress

Zhang, H., Guo, R., Zhang, X., Zhao, C., Wu, J., Xiao, X., Shen, Y., Liu, C., Li, G., Su, K., et al. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1549981 · Cited by 3 · see citing works

Theoretical Study on the Inhibition Mechanism of the Proteasome by Bortezomib

Chen, Y., Song, J., Lan, Y., & Wei, D. (2025) · Communications in Computational Chemistry · doi:10.4208/cicc.2025.203.01 · Cited by 3 · see citing works

Molecular regulation of PGC-1α: from protein-protein interactions and post-translational modifications to pharmacological modulation

Rios, W. Q., Silva, C. M., Ferreira, R. M., & Gomes, J. R. B. (2026) · Journal of Molecular Medicine · doi:10.1007/s00109-026-02694-6 · Cited by 3 · see citing works

A strict requirement in proteasome substrates for spacing between ubiquitin tag and degradation initiation elementsPreprint

Davis, C., Spaller, B. L., Choi, E., Kurrasch, J., Chong, H. C., Elsasser, S., Finley, D. J., & Matouschek, A. T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.08.552540 · Cited by 3 · see citing works

Navigating Solute Carrier Transporters—A Comprehensive Review of Functionalized Small Molecule Probes for Target Identification and Characterization

Dilweg, M. A., Widjaja, T., IJzerman, A. P., & van der Es, D. (2025) · Medicinal Research Reviews · doi:10.1002/med.70009 · Cited by 2 · see citing works

Drosophila proteasome subunit Rpn8 controls IMD pathway activation via PGRP-SC2 degradation

Wu, M., Ali, U., Ding, S., Zhang, C., Jin, Y., Cao, X., Saeed, M. A. R., Zhu, Y., Usama, M., Raza, B., et al. (2025) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2025.104422 · Cited by 2 · see citing works

The SDR1-OsDSK2a-EUI1 module orchestrates plant height and multi-stress resilience in rice

Li, G., Zou, T., Zhang, X., Yang, S., Ma, N., Wang, J., Zhang, X., Xiao, L., Qian, G., Liu, M., et al. (2026) · The Plant Cell · doi:10.1093/plcell/koag119 · Cited by 2 · see citing works

Investigation of the Proteasome 26S Subunit, ATPase Family Genes as Potential Prognostic Biomarkers and Therapeutic Targets for Hepatocellular Carcinoma

Feng, L., Zhang, N., Luo, L., Liu, J., Yao, Y., Gao, M.-S., Pan, J., & He, C. (2024) · Cancer Management and Research · doi:10.2147/cmar.s449488 · Cited by 2 · see citing works

Correlation of disulfidptosis and periodontitis: New insights and clinical significance

Fan, Y., Liu, W., Zhao, Q., Zhao, Q., Li, S., Zou, H., Kong, C., Li, Z., Ren, J., Liu, Z., et al. (2024) · Archives of Oral Biology · doi:10.1016/j.archoralbio.2024.106046 · Cited by 2 · see citing works

Substrate structure determines p97- and RAD23A/B-mediated proteasomal degradation in human cells

Ding, Y., Tomita, T., Tsuchiya, H., & Saeki, Y. (2025) · The Journal of Biochemistry · doi:10.1093/jb/mvaf046 · Cited by 2 · see citing works

The deubiquitinating enzyme USP 8 promotes tyrosine kinase inhibitors resistance in chronic myeloid leukemia by stabilizing EIF 2 S 1 protein

Zhang, S., Lai, H., Bao, W., Liao, C., & Li, J. (2025) · FEBS Journal · doi:10.1111/febs.70300 · Cited by 2 · see citing works

Salt-dependent non-catalytic allostery of human USP14-regulated 26S proteasomePreprint

Zou, S., Zhang, S., Zhao, L., & Mao, Y. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.07.622408 · Cited by 2 · see citing works

The Role of the Proteasome in Limiting Cellular Stress Associated with Protein Accumulation

Kragness, K. A., & Trader, D. J. (2023) · Israel Journal of Chemistry · doi:10.1002/ijch.202300120 · Cited by 1 · see citing works

Nanomaterials exert biological effects by influencing the ubiquitin-proteasome system

Ai, Z., Li, D., Lan, S., & Zhang, C. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116974 · Cited by 1 · see citing works

BQ323636.1 Employs the AR-CCRK Axis to Modulate the Expression of KU70 to Interfere with Non-Homologous End Joining Mediated DNA Repair Mechanism

Tsoi, H., So, Z.-Q., Man, E., You, C., Cheung, K. H.-L., Tse, Y.-S., Chan, W.-L., & Khoo, U. (2025) · Cells · doi:10.3390/cells14171341 · Cited by 1 · see citing works

Mechanism of PP2A affecting ubiquitination pathway in spermatogenesis

Ju, H., Geng, Z., Chen, B., Shang, Y., Chen, X., Wang, D., Wang, W., Sun, H., Shi, Y., & Yu, J. (2025) · Reproductive Biology · doi:10.1016/j.repbio.2025.101167 · Cited by 1 · see citing works

PA28γ, the ring that makes tumors invisible to the immune system?

Cascio, P. (2024) · Biochimie · doi:10.1016/j.biochi.2024.04.003 · Cited by 1 · see citing works

Ubiquitin-Specific Protease 15 Plays an Important Role in Controlling the Tolerance to Salt, Drought and Abscisic Acid in Arabidopsis thaliana

Zou, X., Yin, H., Xie, D., Xu, J., Li, Y., Xiao, W., Liu, S., & Guo, X. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252111569 · Cited by 1 · see citing works

Ubiquitin receptors play redundant roles in the proteasomal degradation of the p53 repressor MDM2

Sparks, A., Kelly, C. J., & Saville, M. K. (2022) · FEBS Letters · doi:10.1002/1873-3468.14436

Liquid–liquid phase separation and biomolecular condensates in cell quiescence

Uversky, V. N. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-823967-4.00001-4

Identifying Essential Deubiquitinase Interactions and Targeting Protein Ubiquitination in Cancer

Gubat, J. (2024) · Linköping University medical dissertations · doi:10.3384/9789180755610

Drug classification for the treatment of hematologic malignancies

Husieva, S. A., Antonyuk, O. Y., & Husieva, V. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-21790-6.00017-1

Antitumor effect of BC12-3 on multiple myeloma via proteasome inhibition

Li, H., Jia, G., Zhang, N., Fan, R., Jia, W., Jin, M., Dan, S., Zhao, W., Jiang, Y., & Kong, D. (2025) · Medical Oncology · doi:10.1007/s12032-025-02804-3

ELITE: E3 Ligase Inference for Tissue specific Elimination: A LLM Based E3 Ligase Prediction System for Precise Targeted Protein DegradationPreprint

Patjoshi, S., Madan, S., & Fröhlich, H. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.05.686884

The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation

Li, H., Guan, H., & Rapoport, T. A. (2026) · Scientific Reports · doi:10.1038/s41598-026-42811-6

Possible Involvement of Differential Ubiquitination as a Molecular Basis of Phenotypic Heterogeneity in Neurodevelopmental Disorders

Nakagawa, T., & Nakagawa, M. (2026) · Genes · doi:10.3390/genes17050553

The Ubiquitin–Proteasome System in Flowering Plant Reproduction: Mechanisms, Functional Diversity, and Regulatory Networks

Jiang, X., Su, H., Chai, M., Yang, F., Cai, H., Qin, Y., & Yan, M. (2026) · Plants · doi:10.3390/plants15101433

The Ubiquitin-Proteasome System: The Cell’s Natural Destroyer

Zhang, Y., Li, X., Shi, L., Wang, H., Li, C., & Liang, L.-J. (2026) · Handbook of experimental pharmacology · doi:10.1007/164_2026_837

Parallel Genomic Responses to Ecological Gradients in the Phalaenopsis amabilis Complex

Sun, P., Huang, Y., Chao, C., Coughlan, J. M., Field, A. R., Nargar, K., Lee, Y., & Liao, P. (2026) · Molecular Ecology · doi:10.1111/mec.70597

It pays to be choosy : mechanisms of substrate selection by the 26S proteasome

Davis, C. (2020) · Texas Digital Library (University of Texas) · doi:10.26153/tsw/60689

Ubiquitin recognition by the proteasome

Saeki, Y. (2016) · The Journal of Biochemistry · doi:10.1093/jb/mvw091 · Cited by 160 · see citing works

Mechanisms and regulation of substrate degradation by the 26S proteasome

Arkinson, C., Dong, K. C., Gee, C. L., & Martin, A. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00778-0 · Cited by 112 · see citing works

Recognition of Client Proteins by the Proteasome

Yu, H., & Matouschek, A. T. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-033719 · Cited by 109 · see citing works

Substrate selection by the proteasome through initiation regions

Tomita, T., & Matouschek, A. T. (2019) · Protein Science · doi:10.1002/pro.3642 · Cited by 37 · see citing works