8YPK

mouse proteasome 20S subunit in complex with compound 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 beta type-6A,
X [auth F]
204Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B [auth P],
K [auth b]
234Mus musculusMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C [auth N],
P [auth I]
248Mus musculusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6D [auth R],
I [auth K]
246Mus musculusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2E [auth T],
J [auth V]
201Mus musculusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1BA [auth X],
F [auth S]
240Mus musculusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5G [auth D],
N [auth C]
204Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for O55234 (Mus musculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3H [auth J],
V [auth Q]
255Mus musculusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1L,
U [auth G]
263Mus musculusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5M [auth H],
R [auth M]
241Mus musculusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4O,
Y [auth Z]
261Mus musculusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7Q [auth B],
T [auth E]
234Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4S [auth W],
W [auth a]
264Mus musculusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3AA [auth U],
Z [auth Y]
205Mus musculusMutation(s): 0 
UniProt
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0258

Structure Validation

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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