8UD9

Structure of human constitutive 20S proteasome complexed with the inhibitor TDI-8304

  • Classification: HYDROLASE/HYDROLASE INHIBITOR
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-09-28 Released: 2023-12-20 
  • Deposition Author(s): Hsu, H.-C., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors.

Hsu, H.C.Li, D.Zhan, W.Ye, J.Liu, Y.J.Leung, A.Qin, J.Crespo, B.Gamo, F.J.Zhang, H.Cui, L.Roth, A.Kirkman, L.A.Li, H.Lin, G.

(2023) Nat Commun 14: 8302-8302

  • DOI: https://doi.org/10.1038/s41467-023-44077-2
  • Primary Citation of Related Structures:  
    8G6E, 8G6F, 8UD9

  • PubMed Abstract: 

    The proteasome of the malaria parasite Plasmodium falciparum (Pf20S) is an advantageous drug target because its inhibition kills P. falciparum in multiple stages of its life cycle and synergizes with artemisinins. We recently developed a macrocyclic peptide, TDI-8304, that is highly selective for Pf20S over human proteasomes and is potent in vitro and in vivo against P. falciparum. A mutation in the Pf20S β6 subunit, A117D, confers resistance to TDI-8304, yet enhances both enzyme inhibition and anti-parasite activity of a tripeptide vinyl sulfone β2 inhibitor, WLW-vs. Here we present the high-resolution cryo-EM structures of Pf20S with TDI-8304, of human constitutive proteasome with TDI-8304, and of Pf20Sβ6 A117D with WLW-vs that give insights into the species selectivity of TDI-8304, resistance to it, and the collateral sensitivity associated with resistance, including that TDI-8304 binds β2 and β5 in wild type Pf20S as well as WLW-vs binds β2 and β5 in Pf20Sβ6 A117D . We further show that TDI-8304 kills P. falciparum as quickly as chloroquine and artemisinin and is active against P. cynomolgi at the liver stage. This increases interest in using these structures to facilitate the development of Pf20S inhibitors that target multiple proteasome subunits and limit the emergence of resistance.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
A, O
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens)
Explore P60900 
Go to UniProtKB:  P60900
PHAROS:  P60900
GTEx:  ENSG00000100902 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60900
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
B, P
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens)
Explore P25787 
Go to UniProtKB:  P25787
PHAROS:  P25787
GTEx:  ENSG00000106588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25787
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
C, Q
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens)
Explore P25789 
Go to UniProtKB:  P25789
PHAROS:  P25789
GTEx:  ENSG00000041357 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25789
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
D, R
248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens)
Explore O14818 
Go to UniProtKB:  O14818
PHAROS:  O14818
GTEx:  ENSG00000101182 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14818
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
E, S
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens)
Explore P28066 
Go to UniProtKB:  P28066
PHAROS:  P28066
GTEx:  ENSG00000143106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28066
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
F, T
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens)
Explore P25786 
Go to UniProtKB:  P25786
PHAROS:  P25786
GTEx:  ENSG00000129084 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25786
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
G, U
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens)
Explore P25788 
Go to UniProtKB:  P25788
PHAROS:  P25788
GTEx:  ENSG00000100567 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25788
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6
H, V
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28072 (Homo sapiens)
Explore P28072 
Go to UniProtKB:  P28072
PHAROS:  P28072
GTEx:  ENSG00000142507 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28072
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7
I, W
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens)
Explore Q99436 
Go to UniProtKB:  Q99436
PHAROS:  Q99436
GTEx:  ENSG00000136930 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99436
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
J, X
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens)
Explore P49720 
Go to UniProtKB:  P49720
PHAROS:  P49720
GTEx:  ENSG00000277791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49720
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
K, Y
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49721 (Homo sapiens)
Explore P49721 
Go to UniProtKB:  P49721
PHAROS:  P49721
GTEx:  ENSG00000126067 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49721
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
L, Z
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens)
Explore P28074 
Go to UniProtKB:  P28074
PHAROS:  P28074
GTEx:  ENSG00000100804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28074
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1AA [auth a],
M
213Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P20618 (Homo sapiens)
Explore P20618 
Go to UniProtKB:  P20618
PHAROS:  P20618
GTEx:  ENSG00000008018 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20618
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4BA [auth b],
N
219Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28070 (Homo sapiens)
Explore P28070 
Go to UniProtKB:  P28070
PHAROS:  P28070
GTEx:  ENSG00000159377 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28070
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YRE (Subject of Investigation/LOI)
Query on YRE

Download Ideal Coordinates CCD File 
CA [auth L],
DA [auth Z]
(7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-dioxo-13-(2-oxopyrrolidin-1-yl)-2-oxa-8,11-diazabicyclo[13.3.1]nonadeca-1(19),15,17-triene-7-carboxamide
C32 H47 N5 O6
UGEFECOTMZPOER-KCHLEUMXSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC4.2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI143714

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-01-03
    Changes: Database references