8YVG

canine immunoproteasome 20S subunit in complex with compound 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Optimization of alpha-amido boronic acids via cryo-electron microscopy analysis: Discovery of a novel highly selective immunoproteasome subunit LMP7 ( beta 5i)/LMP2 ( beta 1i) dual inhibitor.

Arai, Y.Shitama, H.Yamagishi, M.Ono, S.Kashima, A.Hiraizumi, M.Tsuda, N.Katayama, K.Tanaka, K.Koda, Y.Kato, S.Sakata, K.Nureki, O.Miyazaki, H.

(2024) Bioorg Med Chem 109: 117790-117790

  • DOI: https://doi.org/10.1016/j.bmc.2024.117790
  • Primary Citation of Related Structures:  
    8YPK, 8YSX, 8YVG, 8YVP

  • PubMed Abstract: 

    The immunoproteasome subunit LMP7 (β5i)/LMP2 (β1i) dual blockade has been reported to suppress B cell differentiation and activation, suggesting that the dual inhibition of LMP7/LMP2 is a promising approach for treating autoimmune diseases. In contrast, the inhibition of the constitutive proteasome subunit β5c correlates with cytotoxicity against non-immune cells. Therefore, LMP7/LMP2 dual inhibitors with high selectivity over β5c may be desirable for treating autoimmune diseases. In this study, we present the optimization and discovery of α-amido boronic acids using cryo-electron microscopy (cryo-EM). The exploitation of structural differences between the proteasome subunits led to the identification of a highly selective LMP7/LMP2 dual inhibitor 19. Molecular dynamics simulation based on cryo-EM structures of the proteasome subunits complexed with 19 explained the inhibitory activity profile. In mice immunized with 4-hydroxy-3-nitrophenylacetyl conjugated to ovalbumin, results indicate that 19 is orally bioavailable and shows promise as potential treatment for autoimmune diseases.


  • Organizational Affiliation

    Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan. Electronic address: arai.yuuki@ma.mt-pharma.co.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeA [auth M],
K [auth H]
241Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0NHD1 (Canis lupus familiaris)
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UniProt GroupA0A8C0NHD1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeB [auth N],
X [auth I]
248Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0TD63 (Canis lupus familiaris)
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UniProt GroupA0A8C0TD63
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC [auth O],
L [auth Z]
261Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0TIY6 (Canis lupus familiaris)
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UniProt GroupA0A8C0TIY6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeD [auth P],
M [auth b]
234Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0QRK5 (Canis lupus familiaris)
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UniProt GroupA0A8C0QRK5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeE [auth Q],
N [auth J]
255Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0R9W7 (Canis lupus familiaris)
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UniProt GroupA0A8C0R9W7
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaF [auth T],
P [auth V]
201Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0QE86 (Canis lupus familiaris)
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UniProt GroupA0A8C0QE86
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaG [auth U],
Q [auth Y]
205Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0M3N7 (Canis lupus familiaris)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8H [auth C],
Z [auth D]
204Canis lupus familiarisMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q5W416 (Canis lupus familiaris)
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UniProt GroupQ5W416
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth X],
I [auth S]
241Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0N5D2 (Canis lupus familiaris)
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UniProt GroupA0A8C0N5D2
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeJ [auth G],
W [auth L]
263Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PML0 (Canis lupus familiaris)
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UniProt GroupA0A8I3PML0
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeO [auth K],
Y [auth R]
246Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0SR54 (Canis lupus familiaris)
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UniProt GroupA0A8C0SR54
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaR [auth F],
U [auth A]
199Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for Q5W412 (Canis lupus familiaris)
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UniProt GroupQ5W412
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth B],
S [auth E]
273Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0SLB3 (Canis lupus familiaris)
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UniProt GroupA0A8C0SLB3
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaT [auth W],
V [auth a]
264Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8C0MRG6 (Canis lupus familiaris)
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UniProt GroupA0A8C0MRG6
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0258

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 2.0: 2024-10-09
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection