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Yorodumi- EMDB-20877: Allosteric coupling between alpha-rings of the 20S proteasome, ar... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20877 | |||||||||
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Title | Allosteric coupling between alpha-rings of the 20S proteasome, archaea 20S proteasome singly capped with a PAN complex | |||||||||
Map data | Allosteric coupling between alpha-rings of the 20S proteasome, archaea 20S proteasome singly capped with a PAN complex | |||||||||
Sample |
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Keywords | proteasome / PAN / singly-capped / HYDROLASE | |||||||||
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 / endopeptidase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Cheng Y / Yu Z | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Allosteric coupling between α-rings of the 20S proteasome. Authors: Zanlin Yu / Yadong Yu / Feng Wang / Alexander G Myasnikov / Philip Coffino / Yifan Cheng / Abstract: Proteasomal machinery performs essential regulated protein degradation in eukaryotes. Classic proteasomes are symmetric, with a regulatory ATPase docked at each end of the cylindrical 20S. Asymmetric ...Proteasomal machinery performs essential regulated protein degradation in eukaryotes. Classic proteasomes are symmetric, with a regulatory ATPase docked at each end of the cylindrical 20S. Asymmetric complexes are also present in cells, either with a single ATPase or with an ATPase and non-ATPase at two opposite ends. The mechanism that populates these different proteasomal complexes is unknown. Using archaea homologs, we construct asymmetric forms of proteasomes. We demonstrate that the gate conformation of the two opposite ends of 20S are coupled: binding one ATPase opens a gate locally, and also opens the opposite gate allosterically. Such allosteric coupling leads to cooperative binding of proteasomal ATPases to 20S and promotes formation of proteasomes symmetrically configured with two identical ATPases. It may also promote formation of asymmetric complexes with an ATPase and a non-ATPase at opposite ends. We propose that in eukaryotes a similar mechanism regulates the composition of the proteasomal population. | |||||||||
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_20877.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-20877-v30.xml emd-20877.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_20877.png | 70.3 KB | ||
Filedesc metadata | emd-20877.cif.gz | 5.3 KB | ||
Others | emd_20877_additional.map.gz emd_20877_half_map_1.map.gz emd_20877_half_map_2.map.gz | 62.9 MB 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20877 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20877 | HTTPS FTP |
-Validation report
Summary document | emd_20877_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_20877_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_20877_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_20877_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20877 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20877 | HTTPS FTP |
-Related structure data
Related structure data | 6utfMC 6utgC 6uthC 6utiC 6utjC C: citing same article (ref.) M: atomic model generated by this map |
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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_20877.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Allosteric coupling between alpha-rings of the 20S proteasome, archaea 20S proteasome singly capped with a PAN complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_20877_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_20877_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_20877_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : proteasome singly capped with a PAN complex together with GFPssRA...
Entire | Name: proteasome singly capped with a PAN complex together with GFPssRA as a substrate |
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Components |
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-Supramolecule #1: proteasome singly capped with a PAN complex together with GFPssRA...
Supramolecule | Name: proteasome singly capped with a PAN complex together with GFPssRA as a substrate type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
-Macromolecule #1: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 23.169811 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: MNQTLETGTT TVGITLKDAV IMATERRVTM ENFIMHKNGK KLFQIDTYTG MTIAGLVGDA QVLVRYMKAE LELYRLQRRV NMPIEAVAT LLSNMLNQVK YMPYMVQLLV GGIDTAPHVF SIDAAGGSVE DIYASTGSGS PFVYGVLESQ YSEKMTVDEG V DLVIRAIS ...String: MNQTLETGTT TVGITLKDAV IMATERRVTM ENFIMHKNGK KLFQIDTYTG MTIAGLVGDA QVLVRYMKAE LELYRLQRRV NMPIEAVAT LLSNMLNQVK YMPYMVQLLV GGIDTAPHVF SIDAAGGSVE DIYASTGSGS PFVYGVLESQ YSEKMTVDEG V DLVIRAIS AAKQRDSASG GMIDVAVITR KDGYVQLPTD QIESRIRKLG LIL UniProtKB: Proteasome subunit beta |
-Macromolecule #2: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 25.067518 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: AYDRAITVFS PDGRLFQVEY AREAVKKGST ALGMKFANGV LLISDKKVRS RLIEQNSIEA IQLIDDYVAA VTSGLVADAR VLVDFARIS AQQEKVTYGS LVNIENLVKR VADQMQQYTQ YGGVRPYGVS LIFAGIDQIG PRLFDCDPAG TINEYKATAI G SGKDAVVS ...String: AYDRAITVFS PDGRLFQVEY AREAVKKGST ALGMKFANGV LLISDKKVRS RLIEQNSIEA IQLIDDYVAA VTSGLVADAR VLVDFARIS AQQEKVTYGS LVNIENLVKR VADQMQQYTQ YGGVRPYGVS LIFAGIDQIG PRLFDCDPAG TINEYKATAI G SGKDAVVS FLEREYKENL PEKEAVTLGI KALKSSLEEG EELKAPEIAS ITVGNKYRIY DQEEVKKFL UniProtKB: Proteasome subunit alpha |
-Macromolecule #3: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 25.081584 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: AYDRAITVFS PDGRLFQVEY ALEAVKKGST ALGMKFANGV LLISDKKVRS RLIEQNSIEK IQLIDDYVAA VTSGLVADAR VLVDFARIS AQQEKVTYGS LVNIENLVKR VADQMQQYTQ YGGVRPYGVS LIFAGIDQIG PRLFDCDPAG TINEYKATAI G SGKDAVVS ...String: AYDRAITVFS PDGRLFQVEY ALEAVKKGST ALGMKFANGV LLISDKKVRS RLIEQNSIEK IQLIDDYVAA VTSGLVADAR VLVDFARIS AQQEKVTYGS LVNIENLVKR VADQMQQYTQ YGGVRPYGVS LIFAGIDQIG PRLFDCDPAG TINEYKATAI G SGKDAVVS FLEREYKENL PEKEAVTLGI KALKSSLEEG EELKAPEIAS ITVGNKYRIY DQEEVKKFL UniProtKB: Proteasome subunit alpha |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 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: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33000 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |