8CVS

Human PA200-20S proteasome with MG-132


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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-2
A, O
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25789 (Homo sapiens)
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GTEx:  ENSG00000041357 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
C, Q
248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
E, S
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
G, 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-7
H, V
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
J, X
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
K, Y
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
L, 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-4AA [auth a],
M
264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6BA [auth b],
N
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome activator complex subunit 4CA [auth c]1,843Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000068878 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
JA [auth c],
KA [auth c]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
LDZ (Subject of Investigation/LOI)
Query on LDZ

Download Ideal Coordinates CCD File 
DA [auth H]
EA [auth K]
FA [auth N]
GA [auth V]
HA [auth Y]
DA [auth H],
EA [auth K],
FA [auth N],
GA [auth V],
HA [auth Y],
IA [auth b]
N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide
C26 H41 N3 O5
TZYWCYJVHRLUCT-VABKMULXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LDZ BindingDB:  8CVS Ki: min: 1, max: 5520 (nM) from 9 assay(s)
IC50: min: 1.2, max: 4590 (nM) from 20 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-11-02 
  • Deposition Author(s): Zhao, J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection