+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0211 | |||||||||
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Title | 20S proteasome from Archaeoglobus fulgidusProteasome | |||||||||
Map data | 20S control | |||||||||
Sample |
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Function / homology | Function and homology information 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0211.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-0211-v30.xml emd-0211.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_0211.png | 177.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0211 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0211 | HTTPS FTP |
-Related structure data
Related structure data | 6he7MC 0209C 0210C 0212C 0213C 0214C 0215C 0216C 6he4C 6he5C 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_0211.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 20S control | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : 20S proteasome
Entire | Name: 20S proteasomeProteasome |
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Components |
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-Supramolecule #1: 20S proteasome
Supramolecule | Name: 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Archaeoglobus fulgidus DSM 4304 (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 710 KDa |
-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 DSM 4304 (archaea) |
Molecular weight | Theoretical: 26.333248 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ITVFSPDGRL FQVEYAREAV KRGATAIGIK CKEGVILIAD KRVGSKLLEA DTIEKIYKID EHICAATSGL VADARVLIDR ARIEAQINR LTYDEPITVK ELAKKICDFK QQYTQYGGVR PFGVSLLIAG VDEVPKLYET DPSGALLEYK ATAIGMGRNA V TEFFEKEY ...String: ITVFSPDGRL FQVEYAREAV KRGATAIGIK CKEGVILIAD KRVGSKLLEA DTIEKIYKID EHICAATSGL VADARVLIDR ARIEAQINR LTYDEPITVK ELAKKICDFK QQYTQYGGVR PFGVSLLIAG VDEVPKLYET DPSGALLEYK ATAIGMGRNA V TEFFEKEY RDDLSFDDAM VLGLVAMGLS IESELVPENI EVGYVKVDDR TFKEVSPEEL KPYVERANER IRELLKK |
-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 DSM 4304 (archaea) |
Molecular weight | Theoretical: 22.132283 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TTTVGLVCKD GVVMATEKRA TMGNFIASKA AKKIYQIADR MAMTTAGSVG DAQFLARIIK IEANLYEIRR ERKPTVRAIA TLTSNLLNS YRYFPYLVQL LIGGIDSEGK SIYSIDPIGG AIEEKDIVAT GSGSLTAYGV LEDRFTPEIG VDEAVELAVR A IYSAMKRD ...String: TTTVGLVCKD GVVMATEKRA TMGNFIASKA AKKIYQIADR MAMTTAGSVG DAQFLARIIK IEANLYEIRR ERKPTVRAIA TLTSNLLNS YRYFPYLVQL LIGGIDSEGK SIYSIDPIGG AIEEKDIVAT GSGSLTAYGV LEDRFTPEIG VDEAVELAVR A IYSAMKRD SASGDGIDVV KITEDEFYQY SPEEVEQILA KFRK |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: MotionCorr2 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 105384 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6he7: |