+Open data
-Basic information
Entry | Database: PDB / ID: 7ls5 | ||||||
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Title | Cryo-EM structure of the Pre3-1 20S proteasome core particle | ||||||
Components |
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Keywords | HYDROLASE / core particle / complex / assembly intermediate | ||||||
Function / homology | Function and homology information proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å | ||||||
Authors | Schnell, H.M. / Walsh Jr, R.M. / Rawson, S. / Hanna, J.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis. Authors: Helena M Schnell / Richard M Walsh / Shaun Rawson / Mandeep Kaur / Meera K Bhanu / Geng Tian / Miguel A Prado / Angel Guerra-Moreno / Joao A Paulo / Steven P Gygi / Jeroen Roelofs / Daniel Finley / John Hanna / Abstract: The proteasome mediates most selective protein degradation. Proteolysis occurs within the 20S core particle (CP), a barrel-shaped chamber with an αββα configuration. CP biogenesis proceeds ...The proteasome mediates most selective protein degradation. Proteolysis occurs within the 20S core particle (CP), a barrel-shaped chamber with an αββα configuration. CP biogenesis proceeds through an ordered multistep pathway requiring five chaperones, Pba1-4 and Ump1. Using Saccharomyces cerevisiae, we report high-resolution structures of CP assembly intermediates by cryogenic-electron microscopy. The first structure corresponds to the 13S particle, which consists of a complete α-ring, partial β-ring (β2-4), Ump1 and Pba1/2. The second structure contains two additional subunits (β5-6) and represents a later pre-15S intermediate. These structures reveal the architecture and positions of Ump1 and β2/β5 propeptides, with important implications for their functions. Unexpectedly, Pba1's N terminus extends through an open CP pore, accessing the CP interior to contact Ump1 and the β5 propeptide. These results reveal how the coordinated activity of Ump1, Pba1 and the active site propeptides orchestrate key aspects of CP assembly. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ls5.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ls5.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 7ls5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ls5_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7ls5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7ls5_validation.xml.gz | 158.1 KB | Display | |
Data in CIF | 7ls5_validation.cif.gz | 244.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/7ls5 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/7ls5 | HTTPS FTP |
-Related structure data
Related structure data | 23502MC 7ls6C 7lsxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU
#1: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P21243, proteasome endopeptidase complex #2: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P23639, proteasome endopeptidase complex #3: Protein | Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P23638, proteasome endopeptidase complex #4: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P40303, proteasome endopeptidase complex #5: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P32379, proteasome endopeptidase complex #6: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P40302, proteasome endopeptidase complex #7: Protein | Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P21242, proteasome endopeptidase complex |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZM1N2
#8: Protein | Mass: 23631.639 Da / Num. of mol.: 2 / Mutation: G34D / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P38624, proteasome endopeptidase complex #9: Protein | Mass: 28299.889 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P25043, proteasome endopeptidase complex #10: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P25451, proteasome endopeptidase complex #11: Protein | Mass: 24198.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P22141, proteasome endopeptidase complex #12: Protein | Mass: 31670.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P30656, proteasome endopeptidase complex #13: Protein | Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P23724, proteasome endopeptidase complex #14: Protein | Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P30657, proteasome endopeptidase complex |
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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 |
-Sample preparation
Component | Name: 20S / Type: COMPLEX Details: 20S particle purified from Pre3-1 mutant (G34D) via C-terminal Pre1-TEV-ProA affinity tag inserted at the endogenous locus. Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Fluorinated Fos-Choline was added to the sample immediately prior to deposition on a grid for plunge freezing. | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 47169 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.4 sec. / Electron dose: 55.94 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20657 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1633892 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 216361 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4G4S Accession code: 4G4S / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||
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