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- PDB-9y0k: Structure of Plasmodium falciparum 20S proteasome with bound J80 -

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Basic information

Entry
Database: PDB / ID: 9y0k
TitleStructure of Plasmodium falciparum 20S proteasome with bound J80
Components
  • (Proteasome subunit ...) x 13
  • Proteasome endopeptidase complex
KeywordsHYDROLASE/INHIBITOR / Proteasome / 20S proteasome / Plasmodium falciparum / proteasome inhibitor / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / Proteasome assembly / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation ...Cross-presentation of soluble exogenous antigens (endosomes) / Proteasome assembly / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / Neutrophil degranulation / proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteolysis involved in protein catabolic process / peptidase activity / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. ...Proteasome subunit alpha 1 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
: / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome endopeptidase complex / Proteasome subunit beta / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type-6, putative ...: / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome endopeptidase complex / Proteasome subunit beta / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type-6, putative / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit alpha type-1, putative / Proteasome subunit beta
Similarity search - Component
Biological speciesPlasmodium falciparum Dd2 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhang, H. / Zhao, J. / Fajtova, P. / O'Donoghue, A.J.
Funding support United States, European Union, Czech Republic, 12items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH2210520 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI158612 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146387 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI133393 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI171824 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM147487 United States
National Institutes of Health/Office of the DirectorS10 OD026926 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA030199 United States
H2020 Marie Curie Actions of the European Commission846688European Union
European Union (EU)LX22NPO5103European Union
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
European Regional Development FundCZ.02.01.01/00/23_015/0008175European Union
CitationJournal: To Be Published
Title: Structure of Plasmodium falciparum 20S proteasome with bound J80.
Authors: Zhang, H. / Zhao, J. / Fajtova, P. / O'Donoghue, A.J.
History
DepositionAug 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-3
D: Proteasome subunit alpha type-4
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
H: Proteasome endopeptidase complex
I: Proteasome subunit beta-2
J: Proteasome subunit beta-3
K: Proteasome subunit beta-4
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome subunit alpha type-6
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-3
R: Proteasome subunit alpha type-4
S: Proteasome subunit alpha type-5
T: Proteasome subunit alpha type-1
U: Proteasome subunit alpha type-3
V: Proteasome endopeptidase complex
W: Proteasome subunit beta-2
X: Proteasome subunit beta-3
Y: Proteasome subunit beta-4
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)772,07030
Polymers770,51428
Non-polymers1,5562
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Proteasome subunit ... , 13 types, 26 molecules AOBPCQDRESFTGUIWJXKYLZMaNb

#1: Protein Proteasome subunit alpha type-6


Mass: 29531.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_0807500 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8IAR3, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-2


Mass: 26556.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_0608500 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C6KST3
#3: Protein Proteasome subunit alpha type-3


Mass: 27977.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_1353800 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDG3
#4: Protein Proteasome subunit alpha type-4


Mass: 27263.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_1353900 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDG2
#5: Protein Proteasome subunit alpha type-5


Mass: 28417.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PFDG_00127 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0L7LVZ5
#6: Protein Proteasome subunit alpha type-1


Mass: 28871.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_1474800 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IK90
#7: Protein Proteasome subunit alpha type-3


Mass: 29324.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_0317000 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O77396, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta-2


Mass: 25104.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_1328100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I6T3
#10: Protein Proteasome subunit beta-3


Mass: 24533.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_0108000 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I261
#11: Protein Proteasome subunit beta-4


Mass: 22889.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PF3D7_1470900 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IKC9
#12: Protein Proteasome subunit beta


Mass: 23519.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PFTANZ_02851 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024W8G7
#13: Protein Proteasome subunit beta


Mass: 27301.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: CK202_3362, CYL21_3125 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BU46
#14: Protein Proteasome subunit beta


Mass: 34822.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PFDG_00103 / Production host: Spodoptera frugiperda (fall armyworm)

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Protein / Non-polymers , 2 types, 4 molecules HV

#15: Chemical ChemComp-A1CRO / 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


Mass: 777.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H54F3N5O8 / Feature type: SUBJECT OF INVESTIGATION
#8: Protein Proteasome endopeptidase complex


Mass: 29143.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Dd2 (eukaryote) / Gene: PFDG_02566 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0L7M1M6

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: proteasome alpha ring assembly intermediate / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum Dd2 (eukaryote) / Cell: Expi293F / Cellular location: cytoplasm
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCL1
2150 mMsodium chlorideNaCl1
31 mMDTT1
41 mMEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1700 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133662 / Symmetry type: POINT

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