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 9YUY | pdb_00009yuy

Structure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

An Optimized Route to the Syringolin Natural Products Enables Combinatorial Synthesis of Selective, Bioactive Inhibitors of the Plasmodium falciparum 20S Proteasome.

Gu, X., Fajtova, P., Yan, N.L., Saxena, A., Fei, F., Zhu, J., Tse, E., Melo, A., Yoo, E., Buchwald, N.H., Southworth, D.R., Bogyo, M., Derisi, J.L., Gestwicki, J.E., O'Donoghue, A.J., Sello, J.K.

(2026) J Med Chem 69: 8897-8914

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c03223
  • Primary Citation Related Structures: 
    9YUY, 9YUZ

  • PubMed Abstract: 

    The syringolin natural products are covalent inhibitors of the 20S proteasome that inspire therapeutic development. Here, we report a new route to the syringolins amenable to solution and solid-phase synthesis that overcomes a problematic macrocyclization. Exploiting our synthetic approach and substrate mimicry models for proteasome inhibition by the syringolins, we generated a collection of hypothetically selective inhibitors of the Plasmodium falciparum proteasome, which is an emerging target for antimalarial drugs. We identified compounds from the library having high second-order rate constants for Plasmodium proteasome inhibition and nanomolar antiparasitic activity. They exhibited selectivity for the Plasmodium proteasome over the human proteasome. We solved cryo-EM structures of an inhibitor bound to both 20S proteasomes, revealing key contacts favoring species-selective inhibition. Together, this work provides an improved route to syringolin analogs, sheds new light on substrate mimicry by the syringolins, and provides a structural basis for the pursuit of new antimalarial drugs.


  • Organizational Affiliation: 
    • Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.

Macromolecule Content 

  • Total Structure Weight: 794.95 kDa 
  • Atom Count: 50,162 
  • Modeled Residue Count: 6,284 
  • Deposited Residue Count: 6,970 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeA [auth C],
I [auth Q]
246Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1353800
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeB [auth D],
J [auth R]
241Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1353900
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC [auth E],
K [auth S]
256Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0727400
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexD [auth F],
L [auth T]
254Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1474800
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3, putativeE [auth G],
M [auth U]
252Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0317000
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaF [auth K],
N [auth Y]
195Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1470900
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaG [auth L],
O [auth Z]
271Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1011400
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaH [auth M],
P [auth a]
240Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0518300
EC: 3.4.25.1
UniProt
Find proteins for A0A5K1K7U1 (Plasmodium falciparum (isolate 3D7))
Explore A0A5K1K7U1 
Go to UniProtKB:  A0A5K1K7U1
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UniProt GroupA0A5K1K7U1
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexQ [auth A],
W [auth O]
260Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0807500
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexR [auth B],
X [auth P]
235Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0608500
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6, putativeS [auth H],
Y [auth V]
282Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0931800
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaT [auth I],
Z [auth W]
270Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1328100
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth X],
U [auth J]
218Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0108000
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth b],
V [auth N]
265Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0803800
EC: 3.4.25.1
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CY6
(Subject of Investigation/LOI)

Query on A1CY6



Download:Ideal Coordinates CCD File
CA [auth L],
DA [auth Z]
methyl N-{[(2R)-1-({(5R,8R)-5-[(3-fluorophenyl)methyl]-2,7-dioxo-1,6-diazacyclododecan-8-yl}amino)-1-oxo-3-phenylpropan-2-yl]carbamoyl}-L-valinate
C33 H44 F N5 O6
JXWBMCOYNYABKK-GKWDUZDBSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-15
    Type: Initial release
  • Version 1.1: 2026-05-06
    Changes: Data collection, Database references