+Open data
-Basic information
Entry | Database: PDB / ID: 6muw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of the Plasmodium falciparum 20S proteasome. | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / proteasome / protease | |||||||||
Function / homology | Function and homology information 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 / proteasomal ubiquitin-independent protein catabolic process / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / hydrolase activity / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Metcalfe, R.D. / Xie, S.C. / Hanssen, E. / Gillett, D.L. / Leis, A.P. / Tilley, L. / Griffin, M.D.W. | |||||||||
Funding support | Australia, 2items
| |||||||||
Citation | Journal: Nat Microbiol / Year: 2019 Title: The structure of the PA28-20S proteasome complex from Plasmodium falciparum and implications for proteostasis. Authors: Stanley C Xie / Riley D Metcalfe / Eric Hanssen / Tuo Yang / David L Gillett / Andrew P Leis / Craig J Morton / Michael J Kuiper / Michael W Parker / Natalie J Spillman / Wilson Wong / ...Authors: Stanley C Xie / Riley D Metcalfe / Eric Hanssen / Tuo Yang / David L Gillett / Andrew P Leis / Craig J Morton / Michael J Kuiper / Michael W Parker / Natalie J Spillman / Wilson Wong / Christopher Tsu / Lawrence R Dick / Michael D W Griffin / Leann Tilley / Abstract: The activity of the proteasome 20S catalytic core is regulated by protein complexes that bind to one or both ends. The PA28 regulator stimulates 20S proteasome peptidase activity in vitro, but its ...The activity of the proteasome 20S catalytic core is regulated by protein complexes that bind to one or both ends. The PA28 regulator stimulates 20S proteasome peptidase activity in vitro, but its role in vivo remains unclear. Here, we show that genetic deletion of the PA28 regulator from Plasmodium falciparum (Pf) renders malaria parasites more sensitive to the antimalarial drug dihydroartemisinin, indicating that PA28 may play a role in protection against proteotoxic stress. The crystal structure of PfPA28 reveals a bell-shaped molecule with an inner pore that has a strong segregation of charges. Small-angle X-ray scattering shows that disordered loops, which are not resolved in the crystal structure, extend from the PfPA28 heptamer and surround the pore. Using single particle cryo-electron microscopy, we solved the structure of Pf20S in complex with one and two regulatory PfPA28 caps at resolutions of 3.9 and 3.8 Å, respectively. PfPA28 binds Pf20S asymmetrically, strongly engaging subunits on only one side of the core. PfPA28 undergoes rigid body motions relative to Pf20S. Molecular dynamics simulations support conformational flexibility and a leaky interface. We propose lateral transfer of short peptides through the dynamic interface as a mechanism facilitating the release of proteasome degradation products. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6muw.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6muw.ent.gz | 890.1 KB | Display | PDB format |
PDBx/mmJSON format | 6muw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6muw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6muw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6muw_validation.xml.gz | 165.1 KB | Display | |
Data in CIF | 6muw_validation.cif.gz | 252.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/6muw ftp://data.pdbj.org/pub/pdb/validation_reports/mu/6muw | HTTPS FTP |
-Related structure data
Related structure data | 9258MC 9257C 9259C 6dfkC 6muvC 6muxC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-20S proteasome alpha- ... , 7 types, 14 molecules AOBPCQDRESFTGU
#1: Protein | Mass: 29531.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 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) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: C6KST3, proteasome endopeptidase complex #3: Protein | Mass: 27977.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: Q8IDG3, proteasome endopeptidase complex #4: Protein | Mass: 27263.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 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) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: Q8IBI3, proteasome endopeptidase complex #6: Protein | Mass: 28871.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: Q8IK90, proteasome endopeptidase complex #7: Protein | Mass: 29324.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: O77396, proteasome endopeptidase complex |
---|
-20S proteasome beta- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | Mass: 29143.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 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) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 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) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 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) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 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) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: Q8IJT1, proteasome endopeptidase complex #13: Protein | Mass: 27301.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: C0H4E8, proteasome endopeptidase complex #14: Protein | Mass: 30909.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 References: UniProt: Q7K6A9, proteasome endopeptidase complex |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 20S proteasome/PA28 complex. / Type: COMPLEX Details: Sample was a mixture of unbound 20S proteasome, 20S proteasome in complex with one PA28 cap, and 20S proteasome in complex with two PA28 caps. Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.76 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: wait time 0sec blot time 2sec blot force -1 |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5200 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
Image processing | Details: Images were gain corrected | ||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 212749 Details: Relion autopick from 5 class averages resulting from 2000 particle picked manually | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36211 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 54.23 / Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5FMG Accession code: 5FMG / Source name: PDB / Type: experimental model |