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- PDB-9q6f: Structure of Plasmodium falciparum 20S proteasome bound to an asp... -

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Basic information

Entry
Database: PDB / ID: 9q6f
TitleStructure of Plasmodium falciparum 20S proteasome bound to an asparagine-ethylenediamine based inhibitor TDI6245
Components(Proteasome subunit ...) x 14
KeywordsHYDROLASE / Plasmodium falciparum antimalarial proteasome inhibitors
Function / homology
Function and homology information


proteasome core complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / : / proteasomal protein catabolic process / peptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome subunit beta 4 / 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 subunit alpha 1 / Proteasome subunit beta 4 / 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 alpha type / Proteasome subunit alpha type-2 / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Uncharacterized protein / Proteasome alpha-type subunits domain-containing protein / Proteasome alpha-type subunits domain-containing protein ...: / Proteasome subunit alpha type / Proteasome subunit alpha type-2 / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Uncharacterized protein / Proteasome alpha-type subunits domain-containing protein / Proteasome alpha-type subunits domain-containing protein / Proteasome subunit beta / Proteasome alpha-type subunits domain-containing protein / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsHsu, H.C. / Li, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI123794 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143714 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI177635 United States
CitationJournal: To Be Published
Title: Structure-activity relationship study of antimalarial asparagine derived proteasome inhibitors
Authors: Zhang, H. / Hsu, H.C. / Zhan, W. / Hara, R. / Visone, J. / Imaeda, T. / Okamoto, R. / Fajtova, P. / Sato, K. / Michino, M. / Garg, S. / Kreutzfeld, O. / Tumwebaze, P. / Orena, S. / Okitwi, M. ...Authors: Zhang, H. / Hsu, H.C. / Zhan, W. / Hara, R. / Visone, J. / Imaeda, T. / Okamoto, R. / Fajtova, P. / Sato, K. / Michino, M. / Garg, S. / Kreutzfeld, O. / Tumwebaze, P. / Orena, S. / Okitwi, M. / Aso, K. / Cooper, R. / Rosenthal, P.J. / Meinke, P.T. / Foley, M. / ODonoghue, A.J. / Li, H. / Kirkman, L.A. / Lin, G.
History
DepositionAug 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data 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
D: Proteasome subunit alpha type
E: Proteasome subunit alpha type
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
H: Proteasome subunit beta type-6
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
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
R: Proteasome subunit alpha type
S: Proteasome subunit alpha type
T: Proteasome subunit alpha type-1
U: Proteasome subunit alpha type-3
V: Proteasome subunit beta type-6
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)771,45930
Polymers770,45828
Non-polymers1,0012
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 ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZMaNb

#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 (malaria parasite P. falciparum)
Gene: CK202_2446, CYL21_1296, PFNF54_02078 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7JVP8
#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 (malaria parasite P. falciparum)
Gene: CK202_4966, CYL21_4378 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BQ13
#3: Protein Proteasome subunit alpha type


Mass: 27977.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_4303, CYL21_5399, PFNF54_00272 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7KN95
#4: Protein Proteasome subunit alpha type


Mass: 27263.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_4499, CYL21_5482 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BS43
#5: Protein Proteasome subunit alpha type


Mass: 28417.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_5367, CYL21_5183 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BP34
#6: Protein Proteasome subunit alpha type-1


Mass: 28742.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_0007, CYL21_2454, PFNF54_05872 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7K5W7
#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 (malaria parasite P. falciparum)
Gene: CK202_3814, CYL21_3097, PFNF54_00518 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7K040
#8: Protein Proteasome subunit beta type-6


Mass: 29143.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_4201, CYL21_1069, PFNF54_02629 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7JUG8
#9: Protein Proteasome subunit beta


Mass: 25104.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_2690, CYL21_4000, PFNF54_04378 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7K1J4
#10: Protein Proteasome subunit beta


Mass: 24533.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_2185, CYL21_3554 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BXS0
#11: Protein Proteasome subunit beta


Mass: 22889.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_0043, CYL21_2079, PFNF54_05825 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7JKG5
#12: Protein Proteasome subunit beta


Mass: 23620.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CK202_4752, CYL21_3663, PFNF54_02809 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7K6A8
#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 (malaria parasite P. falciparum)
Gene: CK202_3362, CYL21_3125 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / 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 (malaria parasite P. falciparum)
Gene: CK202_2268, CYL21_1305, PFNF54_02044 / Plasmid: pACEBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7K6I2

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Non-polymers , 1 types, 2 molecules

#15: Chemical ChemComp-A1CRS / N~4~-tert-butyl-N~2~-(4-methylbenzene-1-sulfonyl)-N~1~-[2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]-L-aspartamide


Mass: 500.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32N4O5S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: Complex of Plasmodium falciparum 20S with inhibitor TDI-6245
Type: COMPLEX
Details: recombinant Plasmodium falciparum 20S complexed with inhibitor TDI-6245
Entity ID: #1-#14 / Source: RECOMBINANT
Molecular weightValue: 0.7 MDa / Experimental value: NO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 / Plasmid: pACEBac1
Buffer solutionpH: 7.5 / Details: 20 mM Tris, pH 7.5, 5 mM MgCl2, and 100 mM KCl
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.2 sec. / Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 24167
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4particle selection
2SerialEM4image acquisition
7UCSF Chimera1.17model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC4.43D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 17354694
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124807 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 8G6E

8g6e


Accession code: 8G6E / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00251774
ELECTRON MICROSCOPYf_angle_d0.42469916
ELECTRON MICROSCOPYf_dihedral_angle_d4.8976984
ELECTRON MICROSCOPYf_chiral_restr0.0417814
ELECTRON MICROSCOPYf_plane_restr0.0028916

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