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 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    6E5B

  • 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 plasmacytoid d ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2 A, O234Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
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PHAROS:  P25787
GTEx:  ENSG00000106588
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4 B, P261Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
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GTEx:  ENSG00000041357
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7 C, Q248Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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GTEx:  ENSG00000101182
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5 D, R241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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PHAROS:  P28066
GTEx:  ENSG00000143106
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1 E, S263Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
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GTEx:  ENSG00000129084
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3 F, T255Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
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GTEx:  ENSG00000100567
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6 G, U246Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
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GTEx:  ENSG00000100902
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-10 H, V273Homo sapiensMutation(s): 0 
Gene Names: PSMB10, LMP10, MECL1
EC: 3.4.25.1
Find proteins for P40306 (Homo sapiens)
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GTEx:  ENSG00000205220
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3 I, W205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
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GTEx:  ENSG00000277791
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2 J, X201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
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GTEx:  ENSG00000126067
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-8 K, Y276Homo sapiensMutation(s): 0 
Gene Names: PSMB8, LMP7, PSMB5i, RING10, Y2
EC: 3.4.25.1
Find proteins for P28062 (Homo sapiens)
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GTEx:  ENSG00000204264
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1 L, Z241Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
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GTEx:  ENSG00000008018
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4 M, a264Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
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GTEx:  ENSG00000159377
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-9 N, b219Homo sapiensMutation(s): 0 
Gene Names: PSMB9, LMP2, PSMB6i, RING12
EC: 3.4.25.1
Find proteins for P28065 (Homo sapiens)
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GTEx:  ENSG00000240065
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HUJ
Query on HUJ
Download Ideal Coordinates CCD File 
K, N, Y, b
[(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
SCN
Query on SCN
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E, L, Z
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
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G, H, I, K, L, N, U, W, Z, b
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-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 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.573α = 90
b = 203.142β = 106.82
c = 161.487γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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