9Y0K | pdb_00009y0k

Structure of Plasmodium falciparum 20S proteasome with bound J80

PDB DOI: https://doi.org/10.2210/pdb9Y0K/pdb
EM Map EMD-72394: EMDB EMDataResource

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.

Macromolecule Content

Total Structure Weight: 772.07 kDa
Atom Count: 48,226
Modeled Residue Count: 6,248
Deposited Residue Count: 6,780
Unique protein chains: 14

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	A, O	260	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_0807500 EC: 3.4.25.1
UniProt
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7)) Explore Q8IAR3 Go to UniProtKB: Q8IAR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IAR3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	B, P	235	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_0608500
UniProt
Find proteins for C6KST3 (Plasmodium falciparum (isolate 3D7)) Explore C6KST3 Go to UniProtKB: C6KST3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6KST3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	C, Q	246	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_1353800
UniProt
Find proteins for Q8IDG3 (Plasmodium falciparum (isolate 3D7)) Explore Q8IDG3 Go to UniProtKB: Q8IDG3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IDG3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	D, R	241	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_1353900
UniProt
Find proteins for Q8IDG2 (Plasmodium falciparum (isolate 3D7)) Explore Q8IDG2 Go to UniProtKB: Q8IDG2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IDG2
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	E, S	256	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PFDG_00127
UniProt
Find proteins for A0A0L7LVZ5 (Plasmodium falciparum (isolate Dd2)) Explore A0A0L7LVZ5 Go to UniProtKB: A0A0L7LVZ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0L7LVZ5
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	F, T	254	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_1474800 EC: 3.4.25.1
UniProt
Find proteins for Q8IK90 (Plasmodium falciparum (isolate 3D7)) Explore Q8IK90 Go to UniProtKB: Q8IK90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IK90
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	G, U	252	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_0317000 EC: 3.4.25.1
UniProt
Find proteins for O77396 (Plasmodium falciparum (isolate 3D7)) Explore O77396 Go to UniProtKB: O77396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O77396
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome endopeptidase complex	H, V	252	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PFDG_02566
UniProt
Find proteins for A0A0L7M1M6 (Plasmodium falciparum (isolate Dd2)) Explore A0A0L7M1M6 Go to UniProtKB: A0A0L7M1M6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0L7M1M6
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta-2	I, W	229	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_1328100
UniProt
Find proteins for Q8I6T3 (Plasmodium falciparum (isolate 3D7)) Explore Q8I6T3 Go to UniProtKB: Q8I6T3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8I6T3
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta-3	J, X	218	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_0108000
UniProt
Find proteins for Q8I261 (Plasmodium falciparum (isolate 3D7)) Explore Q8I261 Go to UniProtKB: Q8I261
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8I261
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta-4	K, Y	195	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PF3D7_1470900
UniProt
Find proteins for Q8IKC9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IKC9 Go to UniProtKB: Q8IKC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IKC9
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	L, Z	210	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PFTANZ_02851
UniProt
Find proteins for A0A024W8G7 (Plasmodium falciparum Tanzania) Explore A0A024W8G7 Go to UniProtKB: A0A024W8G7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A024W8G7
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	AA [auth a], M	240	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: CK202_3362, CYL21_3125
UniProt
Find proteins for A0A2I0BU46 (Plasmodium falciparum (isolate NF54)) Explore A0A2I0BU46 Go to UniProtKB: A0A2I0BU46
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I0BU46
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	BA [auth b], N	302	Plasmodium falciparum Dd2	Mutation(s): 0 Gene Names: PFDG_00103

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CRO (Subject of Investigation/LOI) Query on A1CRO Download:Ideal Coordinates CCD File SDF format, chain CA [auth L] SDF format, chain DA [auth Z] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth Z] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth Z]	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		Interactions Focus chain CA [auth L] Focus chain DA [auth Z] Interactions & Density Focus chain CA [auth L] Focus chain DA [auth Z]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	W81XWH2210520
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI158612
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21 AI146387
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21 AI133393
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21 AI171824
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM147487
National Institutes of Health/Office of the Director	United States	S10 OD026926
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30 CA030199
H2020 Marie Curie Actions of the European Commission	European Union	846688
European Union (EU)	European Union	LX22NPO5103
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2023042
European Regional Development Fund	European Union	CZ.02.01.01/00/23_015/0008175

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9Y0K | pdb_00009y0k

Structure of Plasmodium falciparum 20S proteasome with bound J80

Literature

Structure of Plasmodium falciparum 20S proteasome with bound J80.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

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Entity ID: 3

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Entity ID: 6

UniProt

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Entity ID: 7

UniProt

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Entity ID: 8

UniProt

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Sequence Annotations

Entity ID: 9

UniProt

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Sequence Annotations

Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)