9Y0K | pdb_00009y0k

Structure of Plasmodium falciparum 20S proteasome with bound J80

  • Classification: HYDROLASE/INHIBITOR
  • Organism(s): Plasmodium falciparum Dd2
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2025-08-28 Released: 2025-10-29 
  • Deposition Author(s): Zhang, H., Zhao, J., Fajtova, P., O'Donoghue, A.J.
  • Funding Organization(s): Department of Defense (DOD, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, National Institutes of Health/National Cancer Institute (NIH/NCI), H2020 Marie Curie Actions of the European Commission, European Union (EU), Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 Plasmodium falciparum 20S proteasome with bound J80.

Zhang, H., Zhao, J., Fajtova, P., O'Donoghue, A.J.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
A, O
260Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_0807500
EC: 3.4.25.1
UniProt
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
B, P
235Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_0608500
UniProt
Find proteins for C6KST3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
C, Q
246Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_1353800
UniProt
Find proteins for Q8IDG3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
D, R
241Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_1353900
UniProt
Find proteins for Q8IDG2 (Plasmodium falciparum (isolate 3D7))
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UniProt GroupQ8IDG2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
E, S
256Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PFDG_00127
UniProt
Find proteins for A0A0L7LVZ5 (Plasmodium falciparum (isolate Dd2))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
F, T
254Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_1474800
EC: 3.4.25.1
UniProt
Find proteins for Q8IK90 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
G, U
252Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_0317000
EC: 3.4.25.1
UniProt
Find proteins for O77396 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complex
H, V
252Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PFDG_02566
UniProt
Find proteins for A0A0L7M1M6 (Plasmodium falciparum (isolate Dd2))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta-2
I, W
229Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_1328100
UniProt
Find proteins for Q8I6T3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta-3
J, X
218Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_0108000
UniProt
Find proteins for Q8I261 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta-4
K, Y
195Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PF3D7_1470900
UniProt
Find proteins for Q8IKC9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
L, Z
210Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PFTANZ_02851
UniProt
Find proteins for A0A024W8G7 (Plasmodium falciparum Tanzania)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth a],
M		240Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: CK202_3362, CYL21_3125
UniProt
Find proteins for A0A2I0BU46 (Plasmodium falciparum (isolate NF54))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth b],
N		302Plasmodium falciparum Dd2Mutation(s): 0 
Gene Names: PFDG_00103
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CRO (Subject of Investigation/LOI)
Query on A1CRO
Download Ideal Coordinates CCD File 
CA [auth L],
DA [auth Z]		N,N-diethyl-N~2~-hexanoyl-D-asparaginyl-N-{(1S)-2-(2,4-difluorophenyl)-1-[(2S,3S,5S,6S)-5-formyl-2-hydroxy-3-(hydroxymethyl)-3,6-dimethylmorpholin-2-yl]ethyl}-4-fluoro-L-phenylalaninamide
C39 H54 F3 N5 O8
ASPQIFKELBCQPZ-KCYJHOJCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH2210520
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI158612
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI146387
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI133393
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI171824
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM147487
National Institutes of Health/Office of the DirectorUnited StatesS10 OD026926
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30 CA030199
H2020 Marie Curie Actions of the European CommissionEuropean Union846688
European Union (EU)European UnionLX22NPO5103
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023042
European Regional Development FundEuropean UnionCZ.02.01.01/00/23_015/0008175

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release