7DR7

bovine 20S immunoproteasome

  • Classification: HYDROLASE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2020-12-26 Released: 2021-01-20 
  • Deposition Author(s): Xu, C., Cong, Y.
  • Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM of mammalian PA28 alpha beta-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28 alpha beta.

Chen, J.Wang, Y.Xu, C.Chen, K.Zhao, Q.Wang, S.Yin, Y.Peng, C.Ding, Z.Cong, Y.

(2021) Nat Commun 12: 739-739

  • DOI: https://doi.org/10.1038/s41467-021-21028-3
  • Primary Citation of Related Structures:  
    7DR6, 7DR7, 7DRW

  • PubMed Abstract: 

    The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, how PA28αβ regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αβ-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determine the spatial arrangement between PA28αβ and iCP through XL-MS. Our structures reveal a slight leaning of PA28αβ towards the α3-α4 side of iCP, disturbing the allosteric network of the gatekeeper α2/3/4 subunits, resulting in a partial open iCP gate. We find that the binding and activation mechanism of iCP by PA28αβ is distinct from those of constitutive CP by the homoheptameric TbPA26 or PfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αβ-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
A, O
248Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3ZBG0 (Bos taurus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
B, P
241Bos taurusMutation(s): 0 
UniProt
Find proteins for Q5E987 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
C, Q
263Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3T0X5 (Bos taurus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
D, R
255Bos taurusMutation(s): 0 
UniProt
Find proteins for Q58DU5 (Bos taurus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
E, L
246Bos taurusMutation(s): 0 
UniProt
Find proteins for Q2YDE4 (Bos taurus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
F, M
234Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3T0Y5 (Bos taurus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
G, N
261Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3ZCK9 (Bos taurus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
H, S
205Bos taurusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P33672 (Bos taurus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
I, T
201Bos taurusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q5E9K0 (Bos taurus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
J, U
241Bos taurusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q2TBX6 (Bos taurus)
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UniProt GroupQ2TBX6
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4
K, V
264Bos taurusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q3T108 (Bos taurus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-9
W, Z
219Bos taurusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q3SZC2 (Bos taurus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-10AA [auth 1],
X
273Bos taurusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8BA [auth 2],
Y
276Bos taurusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q3T112 (Bos taurus)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references