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Structure paper

TitleStructural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 9094, Year 2025
Publish dateOct 15, 2025
AuthorsPiotr Draczkowski / Szu-Ni Chen / Ting Chen / Yong-Sheng Wang / Hsin-An Shih / Jessica Y C Huang / Ming-Chieh Tsai / Shu-Yu Lin / Steven Lin / Rosa Viner / Yuan-Chih Chang / Kuen-Phon Wu / Shang-Te Danny Hsu /
PubMed AbstractBeyond the canonical K48-linked homotypic polyubiquitination for proteasome-targeted proteolysis, K11/K48-branched ubiquitin (Ub) chains are involved in fast-tracking protein turnover during cell ...Beyond the canonical K48-linked homotypic polyubiquitination for proteasome-targeted proteolysis, K11/K48-branched ubiquitin (Ub) chains are involved in fast-tracking protein turnover during cell cycle progression and proteotoxic stress. Here, we report cryo-EM structures of human 26S proteasome in a complex with a K11/K48-branched Ub chain. The structures revealed a multivalent substrate recognition mechanism involving a hitherto unknown K11-linked Ub binding site at the groove formed by RPN2 and RPN10 in addition to the canonical K48-linkage binding site formed by RPN10 and RPT4/5 coiled-coil. Additionally, RPN2 recognizes an alternating K11-K48-linkage through a conserved motif similar to the K48-specific T1 binding site of RPN1. The insights gleaned from these structures explain the molecular mechanism underlying the recognition of the K11/K48-branched Ub as a priority signal in the ubiquitin-mediated proteasomal degradation.
External linksNat Commun / PubMed:41093839 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 4.0 Å
Structure data

36598

8jri

EMDB-36598, PDB-8jri:
Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) without any bound substrate.
Method: EM (single particle) / Resolution: 3.4 Å

36605

8jrt

EMDB-36605, PDB-8jrt:
Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub.
Method: EM (single particle) / Resolution: 3.6 Å

36645

8jti

EMDB-36645, PDB-8jti:
Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
Method: EM (single particle) / Resolution: 3.8 Å

36764

8k0g

EMDB-36764, PDB-8k0g:
Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-37269: Consensus cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub.
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-37273: Local refinement cryo-EM map of human 26S RP (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub, focused on the Ub binding region.
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-37276: Local refinement cryo-EM map of human 26S RP (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub, focused on Rpn3/Rpn7 region.
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-37277: Local refinement cryo-EM map of human 26S RP (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub, focused on AAA+ ATPase subcomplex.
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-37317: Consensus cryo-EM map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-37319: Local refinement cryo-EM map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on the Ub binding region.
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-37327: Local refinement cryo-EM map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on Rpn3/Rpn7 region.
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-37328: Local refinement cryo-EM map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on AAA+ ATPase subcomplex.
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-37334: Consensus cryo-EM map of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-37335: Local refinement cryo-EM map of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on the Ub binding region.
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-37341: Local refinement cryo-EM map of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on the RP lid.
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-37344: Local refinement cryo-EM map of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on AAA+ ATPase subcomplex.
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsCYTOSOLIC PROTEIN / protein degradation / macromolecular complex / ubiquitin-proteasome system

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