+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0209 | |||||||||
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Title | AAA-ATPase ring of PAN-proteasomes | |||||||||
Map data | ATPase ring of PAN in a PAN-proteasome | |||||||||
Sample |
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Keywords | PAN / Proteasome / AAA-ATPase / Archaea / HYDROLASE | |||||||||
Function / homology | Function and homology information proteasome-activating nucleotidase complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) / Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.85 Å | |||||||||
Authors | Majumder P / Rudack T | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0209.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-0209-v30.xml emd-0209.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_0209.png | 139.6 KB | ||
Filedesc metadata | emd-0209.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0209 | HTTPS FTP |
-Validation report
Summary document | emd_0209_validation.pdf.gz | 215.7 KB | Display | EMDB validaton report |
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Full document | emd_0209_full_validation.pdf.gz | 214.8 KB | Display | |
Data in XML | emd_0209_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0209 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0209 | HTTPS FTP |
-Related structure data
Related structure data | 6he4MC 0210C 0211C 0212C 0213C 0214C 0215C 0216C 6he5C 6he7C 6he8C 6he9C 6heaC 6hecC 6hedC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0209.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ATPase ring of PAN in a PAN-proteasome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PAN-proteasome
Entire | Name: PAN-proteasome |
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Components |
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-Supramolecule #1: PAN-proteasome
Supramolecule | Name: PAN-proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Archaeoglobus fulgidus DSM 4304 (archaea) |
Molecular weight | Theoretical: 1.25 MDa |
-Macromolecule #1: Proteasome-activating nucleotidase
Macromolecule | Name: Proteasome-activating nucleotidase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: 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 |
Molecular weight | Theoretical: 29.738418 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KDPMVYGFEV EEKPEVSYED IGGLDVQIEE IREAVELPLL KPELFAEVGI EPPKGVLLYG PPGTGKTLLA KAVANQTRAT FIRVVGSEF VQKYIGEGAR LVREVFQLAK EKAPSIIFID ELDAIAARRT NSDTSGDREV QRTMMQLLAE LDGFDPRGDV K VIGATNRI ...String: KDPMVYGFEV EEKPEVSYED IGGLDVQIEE IREAVELPLL KPELFAEVGI EPPKGVLLYG PPGTGKTLLA KAVANQTRAT FIRVVGSEF VQKYIGEGAR LVREVFQLAK EKAPSIIFID ELDAIAARRT NSDTSGDREV QRTMMQLLAE LDGFDPRGDV K VIGATNRI DILDPAILRP GRFDRIIEVP LPTFEGRIQI FKIHTRKMKL AEDVDFKELA RITEGASGAD IKAICTEAGM FA IREERAK VTMLDFTKAI EKVLKKTTPI UniProtKB: Proteasome-activating nucleotidase |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.1 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 82207 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6he4: |