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 8YVP | pdb_00008yvp

canine immunoproteasome 20S subunit in complex with compound 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8YVP

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: 735.36 kDa 
  • Atom Count: 48,042 
  • Modeled Residue Count: 6,166 
  • Deposited Residue Count: 6,604 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7A [auth B],
K [auth E]
234Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P70195 (Mus musculus)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5B [auth C],
H [auth D]
205Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for O55234 (Mus musculus)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2C [auth P],
P [auth b]
234Mus musculusMutation(s): 0 
UniProt
Find proteins for P49722 (Mus musculus)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3D [auth Q],
I [auth J]
255Mus musculusMutation(s): 0 
UniProt
Find proteins for O70435 (Mus musculus)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6E [auth R],
O [auth K]
246Mus musculusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6F,
Y [auth A]
205Mus musculusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q60692 (Mus musculus)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1G [auth S],
L [auth X]
240Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:104884
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3AA [auth U],
J [auth Y]
205Mus musculusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4BA [auth W],
M [auth a]
264Mus musculusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5N [auth H],
W [auth M]
241Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:1347009
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2Q [auth V],
R [auth T]
201Mus musculusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7S [auth I],
Z [auth N]
248Mus musculusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1T [auth L],
V [auth G]
263Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9R1P4 (Mus musculus)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4U [auth O],
X [auth Z]
261Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9R1P0 (Mus musculus)
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L0D

Query on A1L0D



Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
FA [auth F]
GA [auth D]
IA [auth D]
CA [auth C],
DA [auth C],
FA [auth F],
GA [auth D],
IA [auth D],
JA [auth A]
[(~{R})-cyclohexyl-[(1-cyclohexyl-1,2,3-triazol-4-yl)carbonylamino]methyl]boronic acid
C16 H27 B N4 O3
SSGADSLNPZAYBK-HNNXBMFYSA-N
THR

Query on THR



Download:Ideal Coordinates CCD File
EA [auth C],
HA [auth D]
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A1L0D BindingDB:  8YVP IC50: 4.46e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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, 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: 2024-10-30
    Changes: Data collection