6E5B

Human Immunoproteasome 20S particle in complex with compound 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Design and Evaluation of Highly Selective Human Immunoproteasome Inhibitors Reveal a Compensatory Process That Preserves Immune Cell Viability.

Ladi, E., Everett, C., Stivala, C.E., Daniels, B.E., Durk, M.R., Harris, S.F., Huestis, M.P., Purkey, H.E., Staben, S.T., Augustin, M., Blaesse, M., Steinbacher, S., Eidenschenk, C., Pappu, R., Siu, M.

(2019) J.Med.Chem. 62: 7032-7041

  • DOI: 10.1021/acs.jmedchem.9b00509

  • PubMed Abstract: 

    • The pan-proteasome inhibitor bortezomib demonstrated clinical efficacy in off-label trials of Systemic Lupus Erythematosus. One potential mechanism of this clinical benefit is from the depletion of pathogenic immune cells (plasmablasts and plasmacyto ...

    The pan-proteasome inhibitor bortezomib demonstrated clinical efficacy in off-label trials of Systemic Lupus Erythematosus. One potential mechanism of this clinical benefit is from the depletion of pathogenic immune cells (plasmablasts and plasmacytoid dendritic cells). However, bortezomib is cytotoxic against nonimmune cells, which limits its use for autoimmune diseases. An attractive alternative is to selectively inhibit the immune cell-specific immunoproteasome to deplete pathogenic immune cells and spare nonhematopoietic cells. Here, we disclose the development of highly subunit-selective immunoproteasome inhibitors using insights obtained from the first bona fide human immunoproteasome cocrystal structures. Evaluation of these inhibitors revealed that immunoproteasome-specific inhibition does not lead to immune cell death as anticipated and that targeting viability requires inhibition of both immuno- and constitutive proteasomes. CRISPR/Cas9-mediated knockout experiments confirmed upregulation of the constitutive proteasome upon disruption of the immunoproteasome, protecting cells from death. Thus, immunoproteasome inhibition alone is not a suitable approach to deplete immune cells.

    Organizational Affiliation: 

    Proteros Biostructures GmbH , Bunsenstrasse 7a , Planegg-Martinsried 82152 , Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
A, O
234Homo sapiensMutation(s): 0 
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: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
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: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
C, Q
248Homo sapiensMutation(s): 0 
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: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
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: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
E, S
263Homo sapiensMutation(s): 0 
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: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
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: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
G, U
246Homo sapiensMutation(s): 0 
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: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-10
H, V
273Homo sapiensMutation(s): 0 
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: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
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: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
J, X
201Homo sapiensMutation(s): 0 
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: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-8
K, Y
276Homo sapiensMutation(s): 0 
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: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
L, Z
241Homo sapiensMutation(s): 0 
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: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
M, a
264Homo sapiensMutation(s): 0 
Gene Names: PSMB4 (PROS26)
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to Gene View: PSMB4
Go to UniProtKB:  P28070
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-9
N, b
219Homo sapiensMutation(s): 0 
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
b, G, H, I, K, L, N, U, W, Z
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN
Download SDF File 
Download CCD File 
E, L, Z
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
HUJ
Query on HUJ
Download SDF File 
Download CCD File 
b, K, N, Y
[(1R)-3-methyl-1-[[1-[2-[(2,3,4-trimethoxyphenyl)carbonylamino]ethyl]-1,2,3-triazol-4-yl]carbonylamino]butyl]-tris(oxidanyl)boron
C20 H31 B N5 O8
BKCQATOXENTEDK-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 118.573α = 90.00
b = 203.142β = 106.82
c = 161.487γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release