6AVO image
Deposition Date 2017-09-04
Release Date 2017-12-06
Last Version Date 2025-05-28
Entry Detail
PDB ID:
6AVO
Title:
Cryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-9
Gene (Uniprot):PSMB9
Chain IDs:A, F
Chain Length:219
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-10
Gene (Uniprot):PSMB10
Chain IDs:B, E
Chain Length:234
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-8
Gene (Uniprot):PSMB8
Chain IDs:C, D
Chain Length:204
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-1
Gene (Uniprot):PSMA1
Chain IDs:G, L
Chain Length:263
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-5
Gene (Uniprot):PSMA5
Chain IDs:H, M
Chain Length:241
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-7
Gene (Uniprot):PSMA7
Chain IDs:I, N
Chain Length:248
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-3
Gene (Uniprot):PSMA3
Chain IDs:J, Q
Chain Length:255
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-6
Gene (Uniprot):PSMA6
Chain IDs:K, R
Chain Length:246
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-4
Gene (Uniprot):PSMA4
Chain IDs:O, Z
Chain Length:261
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-2
Gene (Uniprot):PSMA2
Chain IDs:P, BA (auth: b)
Chain Length:234
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-1
Gene (Uniprot):PSMB1
Chain IDs:S, X
Chain Length:213
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-2
Gene (Uniprot):PSMB2
Chain IDs:T, V
Chain Length:201
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-3
Gene (Uniprot):PSMB3
Chain IDs:U, Y
Chain Length:205
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-4
Gene (Uniprot):PSMB4
Chain IDs:W, AA (auth: a)
Chain Length:219
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.
Nat Commun 8 1692 1692 (2017)
PMID: 29167449 DOI: 10.1038/s41467-017-01760-5

Abstact

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.

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Primary Citation of related structures