+Open data
-Basic information
Entry | Database: PDB / ID: 5mpc | ||||||||||||
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Title | 26S proteasome in presence of BeFx (s4) | ||||||||||||
Components |
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Keywords | HYDROLASE / Macromolecular complex / 26S proteasome / Protease | ||||||||||||
Function / homology | Function and homology information SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / negative regulation of proteasomal protein catabolic process / Metalloprotease DUBs / peroxisome fission / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation ...SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / negative regulation of proteasomal protein catabolic process / Metalloprotease DUBs / peroxisome fission / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / protein-containing complex localization / proteasome-activating activity / mitochondrial fission / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / nonfunctional rRNA decay / K48-linked polyubiquitin modification-dependent protein binding / 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 / proteasome binding / peptide catabolic process / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / Ub-specific processing proteases / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / regulation of proteasomal protein catabolic process / ERAD pathway / Neutrophil degranulation / protein folding chaperone / proteasome complex / ubiquitin binding / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / peroxisome / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / chromatin remodeling / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.7 Å | ||||||||||||
Authors | Wehmer, M. / Rudack, T. / Beck, F. / Aufderheide, A. / Pfeifer, G. / Plitzko, J.M. / Foerster, F. / Schulten, K. / Baumeister, W. / Sakata, E. | ||||||||||||
Funding support | Germany, United States, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Structural insights into the functional cycle of the ATPase module of the 26S proteasome. Authors: Marc Wehmer / Till Rudack / Florian Beck / Antje Aufderheide / Günter Pfeifer / Jürgen M Plitzko / Friedrich Förster / Klaus Schulten / Wolfgang Baumeister / Eri Sakata / Abstract: In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where ...In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis. | ||||||||||||
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 | 5mpc.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5mpc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5mpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mpc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5mpc_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5mpc_validation.xml.gz | 362.7 KB | Display | |
Data in CIF | 5mpc_validation.cif.gz | 560.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/5mpc ftp://data.pdbj.org/pub/pdb/validation_reports/mp/5mpc | HTTPS FTP |
-Related structure data
Related structure data | 3537MC 3534C 3535C 3536C 5mp9C 5mpaC 5mpbC 5mpdC 5mpeC 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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1 |
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-Components
-Proteasome subunit alpha type- ... , 6 types, 12 molecules aAbBcCdDeEfF
#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) 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) 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) 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) 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) 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) References: UniProt: P40302, proteasome endopeptidase complex |
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-Protein , 3 types, 4 molecules gGLY
#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) References: UniProt: P21242, proteasome endopeptidase complex #18: Protein | | Mass: 49480.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P53549 #25: Protein | | Mass: 10397.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: O94742 |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules h1i2j3k4l5m6n7
#8: Protein | Mass: 23573.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) 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) References: UniProt: P25451, proteasome endopeptidase complex #11: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) 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) 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) References: UniProt: P30657, proteasome endopeptidase complex |
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-26S protease regulatory subunit ... , 5 types, 5 molecules HIKMJ
#15: Protein | Mass: 52054.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P33299 |
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#16: Protein | Mass: 48898.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40327 |
#17: Protein | Mass: 47953.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P33298 |
#19: Protein | Mass: 48315.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P33297 |
#20: Protein | Mass: 45342.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q01939 |
-26S proteasome regulatory subunit ... , 11 types, 11 molecules WTXZNSPQRUO
#21: Protein | Mass: 29776.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38886 |
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#23: Protein | Mass: 31952.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32496 |
#24: Protein | Mass: 17919.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: O13563 |
#26: Protein | Mass: 109601.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38764 |
#27: Protein | Mass: 104351.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32565 |
#28: Protein | Mass: 60464.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40016 |
#29: Protein | Mass: 51840.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q12250 |
#30: Protein | Mass: 49839.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q12377 |
#31: Protein | Mass: 49016.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q06103 |
#32: Protein | Mass: 38365.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q08723 |
#33: Protein | Mass: 45839.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q04062 |
-Ubiquitin carboxyl-terminal hydrolase ... , 2 types, 2 molecules V8
#22: Protein | Mass: 34442.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P43588, ubiquitinyl hydrolase 1 |
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#34: Protein | Mass: 57188.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P43593, ubiquitinyl hydrolase 1 |
-Non-polymers , 3 types, 12 molecules
#35: Chemical | ChemComp-ATP / #36: Chemical | ChemComp-MG / #37: Chemical | |
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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: 26S proteasome of Saccharomyces cerevisiae in presence of BeFx (s4) Type: COMPLEX / Entity ID: #1-#34 / Source: NATURAL |
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Molecular weight | Value: 1.7 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 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 defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Movie frames/image: 7 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27600 / Symmetry type: POINT |