+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0210 | |||||||||
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Title | 20S core particle of PAN-proteasomes | |||||||||
Map data | 20S alpha-beta of PAN-proteasomes | |||||||||
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 / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process ...proteasome-activating nucleotidase complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol 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: 4.12 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_0210.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-0210-v30.xml emd-0210.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_0210.png | 133.8 KB | ||
Filedesc metadata | emd-0210.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0210 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0210 | HTTPS FTP |
-Validation report
Summary document | emd_0210_validation.pdf.gz | 221.6 KB | Display | EMDB validaton report |
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Full document | emd_0210_full_validation.pdf.gz | 220.8 KB | Display | |
Data in XML | emd_0210_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0210 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0210 | HTTPS FTP |
-Related structure data
Related structure data | 6he5MC 0209C 0211C 0212C 0213C 0214C 0215C 0216C 6he4C 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_0210.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 20S alpha-beta of PAN-proteasomes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: all |
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Source (natural) | Organism: Archaeoglobus fulgidus DSM 4304 (archaea) |
Molecular weight | Theoretical: 1.25 MDa |
-Supramolecule #2: 20S-proteasome
Supramolecule | Name: 20S-proteasome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Archaeoglobus fulgidus DSM 4304 (archaea) |
-Supramolecule #3: Proteasome-activating nucleotidase (PAN)
Supramolecule | Name: Proteasome-activating nucleotidase (PAN) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Archaeoglobus fulgidus DSM 4304 (archaea) |
-Macromolecule #1: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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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: 27.692828 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGHLPQMGYD RAITVFSPDG RLFQVEYARE AVKRGATAIG IKCKEGVILI ADKRVGSKLL EADTIEKIYK IDEHICAATS GLVADARVL IDRARIEAQI NRLTYDEPIT VKELAKKICD FKQQYTQYGG VRPFGVSLLI AGVDEVPKLY ETDPSGALLE Y KATAIGMG ...String: MGHLPQMGYD RAITVFSPDG RLFQVEYARE AVKRGATAIG IKCKEGVILI ADKRVGSKLL EADTIEKIYK IDEHICAATS GLVADARVL IDRARIEAQI NRLTYDEPIT VKELAKKICD FKQQYTQYGG VRPFGVSLLI AGVDEVPKLY ETDPSGALLE Y KATAIGMG RNAVTEFFEK EYRDDLSFDD AMVLGLVAMG LSIESELVPE NIEVGYVKVD DRTFKEVSPE ELKPYVERAN ER IRELLKK UniProtKB: Proteasome subunit alpha |
-Macromolecule #2: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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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: 23.149414 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGTTTVGLVC KDGVVMATEK RATMGNFIAS KAAKKIYQIA DRMAMTTAGS VGDAQFLARI IKIEANLYEI RRERKPTVRA IATLTSNLL NSYRYFPYLV QLLIGGIDSE GKSIYSIDPI GGAIEEKDIV ATGSGSLTAY GVLEDRFTPE IGVDEAVELA V RAIYSAMK ...String: MGTTTVGLVC KDGVVMATEK RATMGNFIAS KAAKKIYQIA DRMAMTTAGS VGDAQFLARI IKIEANLYEI RRERKPTVRA IATLTSNLL NSYRYFPYLV QLLIGGIDSE GKSIYSIDPI GGAIEEKDIV ATGSGSLTAY GVLEDRFTPE IGVDEAVELA V RAIYSAMK RDSASGDGID VVKITEDEFY QYSPEEVEQI LAKFRKHHHH HH UniProtKB: Proteasome subunit beta |
-Macromolecule #3: Proteasome-activating nucleotidase
Macromolecule | Name: Proteasome-activating nucleotidase / type: protein_or_peptide / ID: 3 / 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: 45.279219 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GHMGGDSEIQ YLLEKLKKLE EDYYKLRELY RRLEDEKKFI ESERIRYERE VRRLRSEVER LRSPPLLVGV VSDILEDGRV VVKSSTGPK FVVNTSQYIN EEELKPGARV ALNQQTLAIV NVLPTSKDPM VYGFEVEEKP EVSYEDIGGL DVQIEEIREA V ELPLLKPE ...String: GHMGGDSEIQ YLLEKLKKLE EDYYKLRELY RRLEDEKKFI ESERIRYERE VRRLRSEVER LRSPPLLVGV VSDILEDGRV VVKSSTGPK FVVNTSQYIN EEELKPGARV ALNQQTLAIV NVLPTSKDPM VYGFEVEEKP EVSYEDIGGL DVQIEEIREA V ELPLLKPE LFAEVGIEPP KGVLLYGPPG TGKTLLAKAV ANQTRATFIR VVGSEFVQKY IGEGARLVRE VFQLAKEKAP SI IFIDELD AIAARRTNSD TSGDREVQRT MMQLLAELDG FDPRGDVKVI GATNRIDILD PAILRPGRFD RIIEVPLPTF EGR IQIFKI HTRKMKLAED VDFKELARIT EGASGADIKA ICTEAGMFAI REERAKVTML DFTKAIEKVL KKTTPIPDLK GVMF V UniProtKB: Proteasome-activating nucleotidase |
-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: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 182989 |
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-6he5: |