+Open data
-Basic information
Entry | Database: PDB / ID: 8rvp | ||||||||||||
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Title | Proteasomal late precursor complex from pre1-1, state 2 | ||||||||||||
Components |
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Keywords | HYDROLASE / proteasome biogenesis / Ump1 / pre1-1 / cryo-EM / propertied maturation | ||||||||||||
Function / homology | Function and homology information regulation of proteasome core complex assembly / 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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...regulation of proteasome core complex assembly / 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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / 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 / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / DNA damage response / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.28 Å | ||||||||||||
Authors | Mark, E. / Ramos, P.C. / Kayser, F. / Hoeckendorff, J. / Dohmen, R.J. / Wendler, P. | ||||||||||||
Funding support | Germany, European Union, 3items
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Citation | Journal: Life Sci Alliance / Year: 2024 Title: Structural roles of Ump1 and β-subunit propeptides in proteasome biogenesis. Authors: Eric Mark / Paula C Ramos / Fleur Kayser / Jörg Höckendorff / R Jürgen Dohmen / Petra Wendler / Abstract: The yeast (β4-S142F) mutant accumulates late 20S proteasome core particle precursor complexes (late-PCs). We report a 2.1 Å cryo-EM structure of this intermediate with full-length Ump1 trapped ...The yeast (β4-S142F) mutant accumulates late 20S proteasome core particle precursor complexes (late-PCs). We report a 2.1 Å cryo-EM structure of this intermediate with full-length Ump1 trapped inside, and Pba1-Pba2 attached to the α-ring surfaces. The structure discloses intimate interactions of Ump1 with β2- and β5-propeptides, which together fill most of the antechambers between the α- and β-rings. The β5-propeptide is unprocessed and separates Ump1 from β6 and β7. The β2-propeptide is disconnected from the subunit by autocatalytic processing and localizes between Ump1 and β3. A comparison of different proteasome maturation states reveals that maturation goes along with global conformational changes in the rings, initiated by structuring of the proteolytic sites and their autocatalytic activation. In the strain, β2 is activated first enabling processing of β1-, β6-, and β7-propeptides. Subsequent maturation of β5 and β1 precedes degradation of Ump1, tightening of the complex, and finally release of Pba1-Pba2. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rvp.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rvp.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8rvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rvp_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8rvp_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8rvp_validation.xml.gz | 189.7 KB | Display | |
Data in CIF | 8rvp_validation.cif.gz | 308.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/8rvp ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rvp | HTTPS FTP |
-Related structure data
Related structure data | 19528MC 8rvlC 8rvoC 8rvqC 9gbkC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Proteasome subunit beta type- ... , 7 types, 14 molecules 1M2NHVIWJXKYLZ
#1: Protein | Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23724 #2: Protein | Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30657 #13: Protein | Mass: 23573.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P38624, proteasome endopeptidase complex #14: Protein | Mass: 28313.869 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25043, proteasome endopeptidase complex #15: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25451 #16: Protein | Mass: 24431.629 Da / Num. of mol.: 2 / Mutation: S142F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PRE1, YER012W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22141 #17: Protein | Mass: 31670.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P30656, proteasome endopeptidase complex |
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-Protein , 4 types, 8 molecules 364758GU
#3: Protein | Mass: 16777.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38293 #4: Protein | Mass: 30718.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05778 #5: Protein | Mass: 30762.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36040 #12: Protein | Mass: 31590.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21242 |
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-Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESFT
#6: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243 #7: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23639 #8: Protein | Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23638 #9: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40303 #10: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32379 #11: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40302 |
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-Non-polymers , 1 types, 2016 molecules
#18: Water | ChemComp-HOH / |
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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: Proteasomal late precursor complex from pre1-1 / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 / Details: 150 mM NaCl 50 mM Tris-HCl |
Specimen | Conc.: 0.35 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 R2/4 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K Details: manual plunge freezing device purchased from 'Neptune Fluid Flow Systems' |
-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: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 29904 |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 10556408 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169652 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.74 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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