8JTI image
Deposition Date 2023-06-21
Release Date 2024-12-25
Last Version Date 2025-11-05
Entry Detail
PDB ID:
8JTI
Keywords:
CYTOSOLIC PROTEIN
Title:
Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8JTI validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S protease regulatory subunit 7
Gene (Uniprot):PSMC2
Chain IDs:A
Chain Length:376
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P35998 Pfam ID:PF21236, PF00004, PF17862
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S protease regulatory subunit 4
Gene (Uniprot):PSMC1
Chain IDs:B
Chain Length:377
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62191 Pfam ID:PF16450, PF00004, PF17862
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S protease regulatory subunit 8
Gene (Uniprot):PSMC5
Chain IDs:C
Chain Length:406
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62195 Pfam ID:PF16450, PF00004, PF17862
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S protease regulatory subunit 6B
Gene (Uniprot):PSMC4
Chain IDs:D
Chain Length:350
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P43686 Pfam ID:PF16450, PF00004, PF17862
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S protease regulatory subunit 10B
Gene (Uniprot):PSMC6
Chain IDs:E
Chain Length:389
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62333 Pfam ID:PF16450, PF00004, PF17862
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S protease regulatory subunit 6A
Gene (Uniprot):PSMC3
Chain IDs:F
Chain Length:908
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P17980 Pfam ID:PF16450, PF00004, PF17862
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-6
Gene (Uniprot):PSMA6
Chain IDs:G
Chain Length:246
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60900 Pfam ID:PF10584, PF00227
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-2
Gene (Uniprot):PSMA2
Chain IDs:H
Chain Length:234
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25787 Pfam ID:PF10584, PF00227
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-4
Gene (Uniprot):PSMA4
Chain IDs:I
Chain Length:261
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25789 Pfam ID:PF10584, PF00227 EC:3.4.25.1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-7
Gene (Uniprot):PSMA7
Chain IDs:J
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O14818 Pfam ID:PF10584, PF00227
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-5
Gene (Uniprot):PSMA5
Chain IDs:K
Chain Length:241
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P28066 Pfam ID:PF10584, PF00227
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-1
Gene (Uniprot):PSMA1
Chain IDs:L
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25786 Pfam ID:PF10584, PF00227
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-3
Gene (Uniprot):PSMA3
Chain IDs:M
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P25788 Pfam ID:PF10584, PF00227
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 1
Gene (Uniprot):PSMD1
Chain IDs:N (auth: U)
Chain Length:953
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q99460 Pfam ID:PF21505, PF01851, PF13646, PF18004 EC:5.6.1.5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 3
Gene (Uniprot):PSMD3
Chain IDs:O (auth: V)
Chain Length:534
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43242 Pfam ID:PF08375, PF01399
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 12
Gene (Uniprot):PSMD12
Chain IDs:P (auth: W)
Chain Length:81
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00232 Pfam ID:PF22241, PF01399, PF18098
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 11
Gene (Uniprot):PSMD11
Chain IDs:Q (auth: X)
Chain Length:422
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00231 Pfam ID:PF18055, PF01399, PF18503
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 6
Gene (Uniprot):PSMD6
Chain IDs:R (auth: Y)
Chain Length:389
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15008 Pfam ID:PF10602, PF01399, PF21154
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 7
Gene (Uniprot):PSMD7
Chain IDs:S (auth: Z)
Chain Length:324
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P51665 Pfam ID:PF01398, PF13012
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 13
Gene (Uniprot):PSMD13
Chain IDs:W (auth: a)
Chain Length:376
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UNM6 Pfam ID:PF22037, PF01399
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 4
Gene (Uniprot):PSMD4
Chain IDs:X (auth: b)
Chain Length:377
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P55036 Pfam ID:PF13519, PF02809
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 14
Gene (Uniprot):PSMD14
Chain IDs:Y (auth: c)
Chain Length:406
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00487 Pfam ID:PF01398
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 8
Gene (Uniprot):PSMD8
Chain IDs:T (auth: d)
Chain Length:350
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P48556 Pfam ID:PF10075
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome complex subunit DSS1
Gene (Uniprot):SEM1
Chain IDs:U (auth: e)
Chain Length:389
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60896 Pfam ID:PF05160
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome non-ATPase regulatory subunit 2
Gene (Uniprot):PSMD2
Chain IDs:V (auth: f)
Chain Length:908
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13200 Pfam ID:PF17781, PF01851, PF18051
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polyubiquitin-B
Mutagens:K63R
Chain IDs:Z (auth: v), AA (auth: u), BA (auth: x), CA (auth: w)
Chain Length:953
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P0CG48
Ligand Molecules
ADP
ATP
MG
Primary Citation
Structural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome.
Nat Commun 16 9094 9094 (2025)
PMID: 41093839 DOI: 10.1038/s41467-025-64719-x

Abstact

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.

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Primary Citation of related structures
8JTI