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Open data
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Basic information
Entry | Database: PDB / ID: 6fvu | ||||||
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Title | 26S proteasome, s2 state | ||||||
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![]() | HYDROLASE / 26S proteasome / AAA+ ATPase | ||||||
Function / homology | ![]() SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / maintenance of DNA trinucleotide repeats / filamentous growth ...SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / 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 / metal-dependent deubiquitinase activity / proteasome regulatory particle, base subcomplex / 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 / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / peptide catabolic process / proteasome binding / regulation of protein catabolic process / Orc1 removal from chromatin / protein deubiquitination / 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 / polyubiquitin modification-dependent protein binding / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / enzyme regulator activity / ERAD pathway / protein folding chaperone / Neutrophil degranulation / 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 / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
![]() | Eisele, M.R. / Reed, R.G. / Rudack, T. / Schweitzer, A. / Beck, F. / Nagy, I. / Pfeifer, G. / Plitzko, J.M. / Baumeister, W. / Tomko, R.J. / Sakata, E. | ||||||
![]() | ![]() Title: Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating. Authors: Markus R Eisele / Randi G Reed / Till Rudack / Andreas Schweitzer / Florian Beck / Istvan Nagy / Günter Pfeifer / Jürgen M Plitzko / Wolfgang Baumeister / Robert J Tomko / Eri Sakata / ![]() ![]() Abstract: The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive ...The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into the proteolytic 20S core particle for degradation. Here, we combine genetic and biochemical approaches with cryo-electron microscopy and integrative modeling to dissect the relationship between individual nucleotide binding events and proteasome conformational dynamics. We demonstrate unique impacts of ATP binding by individual ATPases on the proteasome conformational distribution and report two conformational states of the proteasome suggestive of a rotary ATP hydrolysis mechanism. These structures, coupled with functional analyses, reveal key roles for the ATPases Rpt1 and Rpt6 in gating substrate entry into the core particle. This deepened knowledge of proteasome conformational dynamics reveals key elements of intersubunit communication within the proteasome and clarifies the regulation of substrate entry into the proteolytic chamber. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 365.3 KB | Display | |
Data in CIF | ![]() | 558.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3535M ![]() 4321C ![]() 4322C ![]() 4323C ![]() 4324C ![]() 6fvtC ![]() 6fvvC ![]() 6fvwC ![]() 6fvxC ![]() 6fvyC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Proteasome subunit alpha type- ... , 6 types, 12 molecules aAbBcCdDeEfF
#1: Protein | Mass: 27200.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P21243, proteasome endopeptidase complex #2: Protein | Mass: 27060.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P23639, proteasome endopeptidase complex #3: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P23638, proteasome endopeptidase complex #4: Protein | Mass: 28202.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P40303, proteasome endopeptidase complex #5: Protein | Mass: 27442.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P32379, proteasome endopeptidase complex #6: Protein | Mass: 25198.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P40302, proteasome endopeptidase complex |
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-Protein , 2 types, 3 molecules gGV
#7: Protein | Mass: 26734.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P21242, proteasome endopeptidase complex #16: Protein | | Mass: 32490.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P43588, ubiquitinyl hydrolase 1 |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules h1i2j3k4l5m6n7
#8: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P38624, proteasome endopeptidase complex #9: Protein | Mass: 24486.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P25043, proteasome endopeptidase complex #10: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P25451, proteasome endopeptidase complex #11: Protein | Mass: 22218.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P22141, proteasome endopeptidase complex #12: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P30656, proteasome endopeptidase complex #13: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P23724, proteasome endopeptidase complex #14: Protein | Mass: 25832.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P30657, proteasome endopeptidase complex |
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-26S proteasome ... , 18 types, 18 molecules WTXYZNSPQRUOHIKLMJ
#15: Protein | Mass: 21818.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P38886 |
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#17: Protein | Mass: 31111.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P32496 |
#18: Protein | Mass: 14654.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: O13563 |
#19: Protein | Mass: 10397.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: O94742 |
#20: Protein | Mass: 106895.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P38764 |
#21: Protein | Mass: 101894.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P32565 |
#22: Protein | Mass: 55378.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P40016 |
#23: Protein | Mass: 51341.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q12250 |
#24: Protein | Mass: 49839.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q12377 |
#25: Protein | Mass: 46307.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q06103 |
#26: Protein | Mass: 34557.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q08723 |
#27: Protein | Mass: 45194.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q04062 |
#28: Protein | Mass: 47318.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P33299 |
#29: Protein | Mass: 43128.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P40327 |
#30: Protein | Mass: 44353.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P33298 |
#31: Protein | Mass: 43931.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P53549 |
#32: Protein | Mass: 46902.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P33297 |
#33: Protein | Mass: 45342.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q01939 |
-Non-polymers , 3 types, 12 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#34: Chemical | ChemComp-ATP / #35: Chemical | ChemComp-MG / #36: Chemical | ChemComp-ADP / | |
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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: 26S proteasome / Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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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 |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193337 / Symmetry type: POINT |