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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-9
A, F
199Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-10
B, E
234Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-8
C, D
204Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
G, L
263Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
H, M
241Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
I, N
248Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
J, Q
255Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
K, R
246Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
O, Z
261Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
P, b
234Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
S, X
213Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
T, V
201Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
U, Y
205Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
W, a
219Homo sapiensGene 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
IDChainsName / Formula / InChI Key2D Diagram3D 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 NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI70285

Revision History 

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