6AVO

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation  3D Report Full Report


This is version 1.0 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: 10.1038/s41467-017-01760-5

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule Chains Sequence Length Organism Details
Proteasome subunit beta type-9
A, F
199 Homo sapiens Gene Names: PSMB9 (LMP2, PSMB6i, RING12)
EC: 3.4.25.1
Find proteins for P28065 (Homo sapiens)
Go to Gene View: PSMB9
Go to UniProtKB:  P28065
Entity ID: 2
Molecule Chains Sequence Length Organism Details
Proteasome subunit beta type-10
B, E
234 Homo sapiens Gene Names: PSMB10 (LMP10, MECL1)
EC: 3.4.25.1
Find proteins for P40306 (Homo sapiens)
Go to Gene View: PSMB10
Go to UniProtKB:  P40306
Entity ID: 3
Molecule Chains Sequence Length Organism Details
Proteasome subunit beta type-8
C, D
204 Homo sapiens Gene Names: PSMB8 (LMP7, PSMB5i, RING10, Y2)
EC: 3.4.25.1
Find proteins for P28062 (Homo sapiens)
Go to Gene View: PSMB8
Go to UniProtKB:  P28062
Entity ID: 4
Molecule Chains Sequence Length Organism Details
Proteasome subunit alpha type-1
G, L
263 Homo sapiens Gene Names: PSMA1 (HC2, NU, PROS30, PSC2)
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to Gene View: PSMA1
Go to UniProtKB:  P25786
Entity ID: 5
Molecule Chains Sequence Length Organism Details
Proteasome subunit alpha type-5
H, M
241 Homo sapiens Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
Go to Gene View: PSMA5
Go to UniProtKB:  P28066
Entity ID: 6
Molecule Chains Sequence Length Organism Details
Proteasome subunit alpha type-7
I, N
248 Homo sapiens Gene Names: PSMA7 (HSPC)
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to Gene View: PSMA7
Go to UniProtKB:  O14818
Entity ID: 7
Molecule Chains Sequence Length Organism Details
Proteasome subunit alpha type-3
J, Q
255 Homo sapiens Gene Names: PSMA3 (HC8, PSC8)
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
Go to Gene View: PSMA3
Go to UniProtKB:  P25788
Entity ID: 8
Molecule Chains Sequence Length Organism Details
Proteasome subunit alpha type-6
K, R
246 Homo sapiens Gene Names: PSMA6 (PROS27)
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to Gene View: PSMA6
Go to UniProtKB:  P60900
Entity ID: 9
Molecule Chains Sequence Length Organism Details
Proteasome subunit alpha type-4
O, Z
261 Homo sapiens Gene Names: PSMA4 (HC9, PSC9)
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
Go to Gene View: PSMA4
Go to UniProtKB:  P25789
Entity ID: 10
Molecule Chains Sequence Length Organism Details
Proteasome subunit alpha type-2
P, b
234 Homo sapiens Gene Names: PSMA2 (HC3, PSC3)
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
Go to Gene View: PSMA2
Go to UniProtKB:  P25787
Entity ID: 11
Molecule Chains Sequence Length Organism Details
Proteasome subunit beta type-1
S, X
213 Homo sapiens Gene Names: PSMB1 (PSC5)
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
Go to Gene View: PSMB1
Go to UniProtKB:  P20618
Entity ID: 12
Molecule Chains Sequence Length Organism Details
Proteasome subunit beta type-2
T, V
201 Homo sapiens Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
Go to Gene View: PSMB2
Go to UniProtKB:  P49721
Entity ID: 13
Molecule Chains Sequence Length Organism Details
Proteasome subunit beta type-3
U, Y
205 Homo sapiens Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
Go to Gene View: PSMB3
Go to UniProtKB:  P49720
Entity ID: 14
Molecule Chains Sequence Length Organism Details
Proteasome subunit beta type-4
W, a
219 Homo sapiens Gene Names: PSMB4 (PROS26)
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to Gene View: PSMB4
Go to UniProtKB:  P28070
Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BZ7
Query on BZ7

Download SDF File 
Download CCD File 
C, D
N~1~-{2-[([1,1'-biphenyl]-3-carbonyl)amino]ethyl}-N~4~-tert-butyl-N~2~-(3-phenylpropanoyl)-L-aspartamide
PKS21004
C32 H38 N4 O4
ZMFRLEFFYGXGES-MHZLTWQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software Name Purpose
PHENIX refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding Organization Country Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases United States R01 AI70285

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release