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Yorodumi- EMDB-1740: Mechanism of Gate Opening in the 20S proteasome by the proteasoma... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1740 | |||||||||
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Title | Mechanism of Gate Opening in the 20S proteasome by the proteasomal ATPases | |||||||||
Map data | Archaeal 20S proteasome with a closed gate | |||||||||
Sample |
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Keywords | 20S proteasome from Thermoplasma acidophilum with a closed gate | |||||||||
Function / homology | Function and homology information proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / endopeptidase activity / ubiquitin-dependent protein catabolic process / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Rabl J / Smith DM / Yu Y / Chang SC / Goldberg AL / Cheng Y | |||||||||
Citation | Journal: Mol Cell / Year: 2008 Title: Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Authors: Julius Rabl / David M Smith / Yadong Yu / Shih-Chung Chang / Alfred L Goldberg / Yifan Cheng / Abstract: Substrates enter the cylindrical 20S proteasome through a gated channel that is regulated by the ATPases in the 19S regulatory particle in eukaryotes or the homologous PAN ATPase complex in archaea. ...Substrates enter the cylindrical 20S proteasome through a gated channel that is regulated by the ATPases in the 19S regulatory particle in eukaryotes or the homologous PAN ATPase complex in archaea. These ATPases contain a conserved C-terminal hydrophobic-tyrosine-X (HbYX) motif that triggers gate opening upon ATP binding. Using cryo-electron microscopy, we identified the sites in the archaeal 20S where PAN's C-terminal residues bind and determined the structures of the gate in its closed and open forms. Peptides containing the HbYX motif bind to 20S in the pockets between neighboring alpha subunits where they interact with conserved residues required for gate opening. This interaction induces a rotation in the alpha subunits and displacement of a reverse-turn loop that stabilizes the open-gate conformation. This mechanism differs from that of PA26/28, which lacks the HbYX motif and does not cause alpha subunit rotation. These findings demonstrated how the ATPases' C termini function to facilitate substrate entry. | |||||||||
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_1740.map.gz | 10.5 MB | EMDB map data format | |
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Header (meta data) | emd-1740-v30.xml emd-1740.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd1740.tif | 537.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1740 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1740 | HTTPS FTP |
-Validation report
Summary document | emd_1740_validation.pdf.gz | 388.8 KB | Display | EMDB validaton report |
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Full document | emd_1740_full_validation.pdf.gz | 388.3 KB | Display | |
Data in XML | emd_1740_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1740 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1740 | HTTPS FTP |
-Related structure data
Related structure data | 3c92MC 1733C 3c91C 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_1740.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Archaeal 20S proteasome with a closed gate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36825 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 : Thermoplasma acidophilum 20S proteasome
Entire | Name: Thermoplasma acidophilum 20S proteasome |
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Components |
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-Supramolecule #1000: Thermoplasma acidophilum 20S proteasome
Supramolecule | Name: Thermoplasma acidophilum 20S proteasome / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1 |
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Molecular weight | Experimental: 700 KDa / Theoretical: 700 KDa |
-Macromolecule #1: Archaeal 20S proteasome
Macromolecule | Name: Archaeal 20S proteasome / type: protein_or_peptide / ID: 1 / Name.synonym: Archaeal 20S proteasome / Number of copies: 14 / Oligomeric state: 4 rings of heptamer / Recombinant expression: Yes |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Experimental: 700 KDa / Theoretical: 700 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Grid | Details: 400 Quantifoil |
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Vitrification | Cryogen name: NITROGEN / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Details | Low Dose |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side-entry cryoholder / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each Particle |
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Final reconstruction | Applied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-3c92: |