7PG9

human 20S proteasome

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-08-13 Released: 2021-10-20 
  • Deposition Author(s): Xu, C., Cong, Y.
  • Funding Organization(s): Israel Science Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag.

Sahu, I.Mali, S.M.Sulkshane, P.Xu, C.Rozenberg, A.Morag, R.Sahoo, M.P.Singh, S.K.Ding, Z.Wang, Y.Day, S.Cong, Y.Kleifeld, O.Brik, A.Glickman, M.H.

(2021) Nat Commun 12: 6173-6173

  • DOI: https://doi.org/10.1038/s41467-021-26427-0
  • Primary Citation of Related Structures:  
    7PG9, 7V5G, 7V5M

  • PubMed Abstract: 

    The proteasome, the primary protease for ubiquitin-dependent proteolysis in eukaryotes, is usually found as a mixture of 30S, 26S, and 20S complexes. These complexes have common catalytic sites, which makes it challenging to determine their distinctive roles in intracellular proteolysis. Here, we chemically synthesize a panel of homogenous ubiquitinated proteins, and use them to compare 20S and 26S proteasomes with respect to substrate selection and peptide-product generation. We show that 20S proteasomes can degrade the ubiquitin tag along with the conjugated substrate. Ubiquitin remnants on branched peptide products identified by LC-MS/MS, and flexibility in the 20S gate observed by cryo-EM, reflect the ability of the 20S proteasome to proteolyze an isopeptide-linked ubiquitin-conjugate. Peptidomics identifies proteasome-trapped ubiquitin-derived peptides and peptides of potential 20S substrates in Hi20S cells, hypoxic cells, and human failing-heart. Moreover, elevated levels of 20S proteasomes appear to contribute to cell survival under stress associated with damaged proteins.


  • Organizational Affiliation

    Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel. glickman@technion.ac.il.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
A, O
246Homo sapiensMutation(s): 0 
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PHAROS:  P60900
GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
B, P
234Homo sapiensMutation(s): 0 
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Find proteins for P25787 (Homo sapiens)
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
C, Q
261Homo sapiensMutation(s): 0 
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Find proteins for P25789 (Homo sapiens)
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GTEx:  ENSG00000041357 
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UniProt GroupP25789
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
D, R
248Homo sapiensMutation(s): 0 
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Find proteins for O14818 (Homo sapiens)
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GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
E, S
241Homo sapiensMutation(s): 0 
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Find proteins for P28066 (Homo sapiens)
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GTEx:  ENSG00000143106 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
F, T
263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000129084 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
G, U
255Homo sapiensMutation(s): 0 
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Find proteins for P25788 (Homo sapiens)
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GTEx:  ENSG00000100567 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6
H, V
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28072 (Homo sapiens)
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GTEx:  ENSG00000142507 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7
I, W
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for Q99436 (Homo sapiens)
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GTEx:  ENSG00000136930 
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UniProt GroupQ99436
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
J, X
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P49720 (Homo sapiens)
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GTEx:  ENSG00000277791 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
K, Y
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
L, Z
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28074 (Homo sapiens)
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GTEx:  ENSG00000100804 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1AA [auth a],
M
213Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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UniProt GroupP20618
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4BA [auth b],
N
219Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references