+Open data
-Basic information
Entry | Database: PDB / ID: 6he5 | ||||||
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Title | 20S core particle of PAN-proteasomes | ||||||
Components |
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Keywords | HYDROLASE / PAN / Proteasome / AAA-ATPase / Archaea | ||||||
Function / homology | Function and homology information proteasome-activating nucleotidase 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 / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process ...proteasome-activating nucleotidase 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 / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.12 Å | ||||||
Authors | Majumder, P. / Rudack, T. / Beck, F. / Baumeister, W. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 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. | ||||||
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 | 6he5.cif.gz | 557.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6he5.ent.gz | 427.3 KB | Display | PDB format |
PDBx/mmJSON format | 6he5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6he5_validation.pdf.gz | 918.5 KB | Display | wwPDB validaton report |
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Full document | 6he5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6he5_validation.xml.gz | 93.5 KB | Display | |
Data in CIF | 6he5_validation.cif.gz | 139.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/6he5 ftp://data.pdbj.org/pub/pdb/validation_reports/he/6he5 | HTTPS FTP |
-Related structure data
Related structure data | 0210MC 0209C 0211C 0212C 0213C 0214C 0215C 0216C 6he4C 6he7C 6he8C 6he9C 6heaC 6hecC 6hedC 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
#1: Protein | Mass: 27692.828 Da / Num. of mol.: 7 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: psmA, AF_0490 / Production host: Escherichia coli (E. coli) References: UniProt: O29760, proteasome endopeptidase complex #2: Protein | Mass: 23149.414 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: psmB, AF_0481 / Production host: Escherichia coli (E. coli) References: UniProt: Q9P996, proteasome endopeptidase complex #3: Protein | Mass: 45279.219 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: pan, AF_1976 / Production host: Escherichia coli (E. coli) / References: UniProt: O28303 |
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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 |
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Molecular weight | Value: 1.25 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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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 |
-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 |
Image recording | Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182989 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |