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Open data
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Basic information
Entry | Database: PDB / ID: 8w2f | |||||||||||||||
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Title | Plasmodium falciparum 20S proteasome bound to an inhibitor | |||||||||||||||
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![]() | CYTOSOLIC PROTEIN/INHIBITOR / Malaria / Plasmodium falciparum / proteasome / drug discovery / CYTOSOLIC PROTEIN / CYTOSOLIC PROTEIN-INHIBITOR complex | |||||||||||||||
Function / homology | ![]() Cross-presentation of soluble exogenous antigens (endosomes) / 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 / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation ...Cross-presentation of soluble exogenous antigens (endosomes) / 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 / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / 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 / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / hydrolase activity / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
![]() | Han, Y. / Deng, X. / Ray, S. / Chen, Z. / Phillips, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of potent and reversible piperidine carboxamides that are species-selective orally active proteasome inhibitors to treat malaria Authors: Lawong, A. / Gahalawat, S. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 158.9 KB | Display | |
Data in CIF | ![]() | 245.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 43746MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Proteasome endopeptidase ... , 3 types, 6 molecules AOBPFT
#1: Protein | Mass: 29531.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8IAR3, proteasome endopeptidase complex #2: Protein | Mass: 26556.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: C6KST3, proteasome endopeptidase complex #6: Protein | Mass: 28871.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8IK90, proteasome endopeptidase complex |
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-Proteasome subunit ... , 11 types, 22 molecules CQDRESGUHVIWJXKYLZNbMa
#3: Protein | Mass: 27443.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 27263.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8IDG2, proteasome endopeptidase complex #5: Protein | Mass: 28417.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8IBI3, proteasome endopeptidase complex #7: Protein | Mass: 29324.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O77396, proteasome endopeptidase complex #8: Protein | Mass: 29143.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8I0U7, proteasome endopeptidase complex #9: Protein | Mass: 25104.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8I6T3, proteasome endopeptidase complex #10: Protein | Mass: 24533.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8I261, proteasome endopeptidase complex #11: Protein | Mass: 22889.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8IKC9, proteasome endopeptidase complex #12: Protein | Mass: 23620.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q8IJT1, proteasome endopeptidase complex #13: Protein | Mass: 33155.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: tag was introduced using the CRISPR/Cas9 system at the endogenous locus Source: (gene. exp.) ![]() ![]() ![]() ![]() #14: Protein | Mass: 27301.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A5K1K7U1, proteasome endopeptidase complex |
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-Non-polymers , 1 types, 2 molecules
#15: Chemical | Mass: 420.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25FN4O3S / Feature type: SUBJECT OF INVESTIGATION |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Plasmodium falciparum 20S proteasome bound with an inhibitor Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.75 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||
Buffer solution | pH: 7.6 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1074710 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20317 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5FMG Accession code: 5FMG / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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