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


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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: 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 sub ...

    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

    Department of Microbiology & Immunology, Weill Cornell Medicine, New York, NY, 10065, USA. gal2005@med.cornell.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-9 AF199Homo sapiensMutation(s): 0 
Gene Names: PSMB9LMP2PSMB6iRING12
EC: 3.4.25.1
Find proteins for P28065 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-10 BE234Homo sapiensMutation(s): 0 
Gene Names: PSMB10LMP10MECL1
EC: 3.4.25.1
Find proteins for P40306 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-8 CD204Homo sapiensMutation(s): 0 
Gene Names: PSMB8LMP7PSMB5iRING10Y2
EC: 3.4.25.1
Find proteins for P28062 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1 GL263Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5 HM241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7 IN248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3 JQ255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6 KR246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4 OZ261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2 Pb234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1 SX213Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2 TV201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3 UY205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4 Wa219Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BZ7
Query on BZ7

Download Ideal Coordinates CCD File 
C, 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence