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Open data
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Basic information
Entry | Database: PDB / ID: 6hed | ||||||
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Title | PAN-proteasome in state 5 | ||||||
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![]() | HYDROLASE / PAN / Proteasome / AAA-ATPase / Archaea | ||||||
Function / homology | ![]() proteasome-activating nucleotidase complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity ...proteasome-activating nucleotidase complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.95 Å | ||||||
![]() | Majumder, P. / Rudack, T. / Beck, F. / Baumeister, W. | ||||||
![]() | ![]() Title: Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle. Authors: Parijat Majumder / Till Rudack / Florian Beck / Radostin Danev / Günter Pfeifer / István Nagy / Wolfgang Baumeister / ![]() Abstract: Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein ...Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein homeostasis, and control vital cellular processes. While the eukaryotic 26S proteasome is extensively characterized, its putative evolutionary precursor, the archaeal proteasome, remains poorly understood. The primordial archaeal proteasome consists of a 20S proteolytic core particle (CP), and an AAA-ATPase module. This minimal complex degrades protein unassisted by non-ATPase subunits that are present in a 26S proteasome regulatory particle (RP). Using cryo-EM single-particle analysis, we determined structures of the archaeal CP in complex with the AAA-ATPase PAN (proteasome-activating nucleotidase). Five conformational states were identified, elucidating the functional cycle of PAN, and its interaction with the CP. Coexisting nucleotide states, and correlated intersubunit signaling features, coordinate rotation of the PAN-ATPase staircase, and allosterically regulate N-domain motions and CP gate opening. These findings reveal the structural basis for a sequential around-the-ring ATPase cycle, which is likely conserved in AAA-ATPases. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 232.8 KB | Display | |
Data in CIF | ![]() | 347.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0216MC ![]() 0209C ![]() 0210C ![]() 0211C ![]() 0212C ![]() 0213C ![]() 0214C ![]() 0215C ![]() 6he4C ![]() 6he5C ![]() 6he7C ![]() 6he8C ![]() 6he9C ![]() 6heaC ![]() 6hecC 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 ... , 2 types, 28 molecules AaBbCcDdEeFfGg1h2i3j4k5l6m7n
#1: Protein | Mass: 27156.160 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: psmA, AF_0490 / Production host: ![]() ![]() References: UniProt: O29760, proteasome endopeptidase complex #2: Protein | Mass: 22132.283 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: psmB, AF_0481 / Production host: ![]() ![]() References: UniProt: Q9P996, proteasome endopeptidase complex |
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-Protein , 1 types, 6 molecules HIKLMJ
#3: Protein | Mass: 44102.977 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pan, AF_1976 / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 10 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)
#4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-MG / #6: 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
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Molecular weight | Value: 1.25 MDa / Experimental value: NO | ||||||||||||||||||||||||
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Buffer solution | pH: 7.1 | ||||||||||||||||||||||||
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: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 6.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30758 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |