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 8YSX | pdb_00008ysx

canine immunoproteasome 20S subunit in complex with compound 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 732.36 kDa 
  • Atom Count: 47,878 
  • Modeled Residue Count: 6,158 
  • Deposited Residue Count: 6,592 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaA [auth F],
X [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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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeB [auth L],
S [auth G]
263Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PCT4 (Canis lupus familiaris)
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UniProt GroupA0A8I3PCT4
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC [auth M],
M [auth H]
241Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3N3S4 (Canis lupus familiaris)
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UniProt GroupA0A8I3N3S4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeD [auth N],
N [auth I]
248Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3NW81 (Canis lupus familiaris)
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UniProt GroupA0A8I3NW81
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeE [auth O],
R [auth Z]
261Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3NP66 (Canis lupus familiaris)
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UniProt GroupA0A8I3NP66
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeF [auth R],
Y [auth K]
246Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3N0P1 (Canis lupus familiaris)
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UniProt GroupA0A8I3N0P1
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaG [auth T],
P [auth V]
201Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3NUC6 (Canis lupus familiaris)
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UniProt GroupA0A8I3NUC6
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaH [auth U],
Q [auth Y]
205Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3RXV3 (Canis lupus familiaris)
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UniProt GroupA0A8I3RXV3
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaI [auth a],
U [auth W]
264Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PII7 (Canis lupus familiaris)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8J [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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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeAA [auth P],
K [auth b]
234Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PCE5 (Canis lupus familiaris)
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UniProt GroupA0A8I3PCE5
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth S],
L [auth X]
241Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PKH4 (Canis lupus familiaris)
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UniProt GroupA0A8I3PKH4
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeO [auth J],
W [auth Q]
255Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3P0V3 (Canis lupus familiaris)
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UniProt GroupA0A8I3P0V3
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaT [auth E],
V [auth B]
234Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3RZF7 (Canis lupus familiaris)
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UniProt GroupA0A8I3RZF7
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
  • Version 2.0: 2024-10-09
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Database references, Derived calculations, Experimental preparation, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection