7NAP

Human PA28-20S-PA28 proteasome complex

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

  • Deposited: 2021-06-22 Released: 2022-11-02 
  • Deposition Author(s): Zhao, J., Makhija, S., Huang, B., Cheng, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins.

Zhao, J.Makhija, S.Zhou, C.Zhang, H.Wang, Y.Muralidharan, M.Huang, B.Cheng, Y.

(2022) Proc Natl Acad Sci U S A 119: e2207200119-e2207200119

  • DOI: https://doi.org/10.1073/pnas.2207200119
  • Primary Citation of Related Structures:  
    7NAN, 7NAO, 7NAP, 7NAQ, 8CVR, 8CVS, 8CVT, 8CXB

  • PubMed Abstract: 

    The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αβ-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4β engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A [auth O],
V [auth A]
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B [auth P],
W [auth B]
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25789 (Homo sapiens)
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PHAROS:  P25789
GTEx:  ENSG00000041357 
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UniProt GroupP25789
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C [auth Q],
X [auth C]
248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for O14818 (Homo sapiens)
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PHAROS:  O14818
GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D [auth R],
Y [auth D]
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28066 (Homo sapiens)
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GTEx:  ENSG00000143106 
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UniProt GroupP28066
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E [auth S],
Z [auth E]
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25786 (Homo sapiens)
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GTEx:  ENSG00000129084 
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UniProt GroupP25786
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3AA [auth F],
F [auth T]
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25788 (Homo sapiens)
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GTEx:  ENSG00000100567 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6BA [auth G],
G [auth U]
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P60900 (Homo sapiens)
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GTEx:  ENSG00000100902 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7CA [auth H],
H [auth V]
277Homo 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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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3DA [auth I],
I [auth W]
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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UniProt GroupP49720
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2EA [auth J],
J [auth X]
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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UniProt GroupP49721
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5FA [auth K],
K [auth Y]
263Homo 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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1GA [auth L],
L [auth Z]
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4HA [auth M],
M [auth a]
264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28070 (Homo sapiens)
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GTEx:  ENSG00000159377 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6IA [auth N],
N [auth b]
239Homo 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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UniProt GroupP28072
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome activator complex subunit 2239Homo sapiensMutation(s): 0 
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Find proteins for Q9UL46 (Homo sapiens)
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GTEx:  ENSG00000100911 
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UniProt GroupQ9UL46
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome activator complex subunit 1249Homo sapiensMutation(s): 0 
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Find proteins for Q06323 (Homo sapiens)
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GTEx:  ENSG00000092010 
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UniProt GroupQ06323
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM140847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM124334
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM131641

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Data collection