6AVO

Cryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.

Santos, R.L.A.Bai, L.Singh, P.K.Murakami, N.Fan, H.Zhan, W.Zhu, Y.Jiang, X.Zhang, K.Assker, J.P.Nathan, C.F.Li, H.Azzi, J.Lin, G.

(2017) Nat Commun 8: 1692-1692

  • DOI: https://doi.org/10.1038/s41467-017-01760-5
  • Primary Citation of Related Structures:  
    6AVO

  • PubMed Abstract: 

    Proteasome inhibitors benefit patients with multiple myeloma and B cell-dependent autoimmune disorders but exert toxicity from inhibition of proteasomes in other cells. Toxicity should be minimized by reversible inhibition of the immunoproteasome β5i subunit while sparing the constitutive β5c subunit. Here we report β5i-selective inhibition by asparagine-ethylenediamine (AsnEDA)-based compounds and present the high-resolution cryo-EM structural analysis of the human immunoproteasome. Despite inhibiting noncompetitively, an AsnEDA inhibitor binds the active site. Hydrophobic interactions are accompanied by hydrogen bonding with β5i and β6 subunits. The inhibitors are far more cytotoxic for myeloma and lymphoma cell lines than for hepatocarcinoma or non-activated lymphocytes. They block human B-cell proliferation and promote apoptotic cell death selectively in antibody-secreting B cells, and to a lesser extent in activated human T cells. Reversible, β5i-selective inhibitors may be useful for treatment of diseases involving activated or neoplastic B cells or activated T cells.


  • Organizational Affiliation

    Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-9
A, F
199Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000240065 
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UniProt GroupP28065
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-10
B, E
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000205220 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-8
C, D
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000204264 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
G, L
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
H, M
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
I, N
248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
J, Q
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
K, R
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
O, Z
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2BA [auth b],
P
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
S, X
213Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
T, V
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
U, Y
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth a],
W
219Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BZ7
Query on BZ7

Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth D]
N~1~-{2-[([1,1'-biphenyl]-3-carbonyl)amino]ethyl}-N~4~-tert-butyl-N~2~-(3-phenylpropanoyl)-L-aspartamide
C32 H38 N4 O4
ZMFRLEFFYGXGES-MHZLTWQESA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI70285

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references