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Yorodumi- EMDB-20879: Allosteric coupling between alpha-rings of 20S proteasome, 20S pr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20879 | |||||||||
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Title | Allosteric coupling between alpha-rings of 20S proteasome, 20S proteasome singly capped with a PA26/E102A_PANc, together with LFP incubation | |||||||||
Map data | Allosteric coupling between alpha-rings of 20S proteasome, 20S proteasome singly capped with a PA26/E102A_PANc, together with LFP incubation | |||||||||
Sample |
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Keywords | PA26PANc / proteasome / substrate LFP / HYDROLASE | |||||||||
Function / homology | Function and homology information proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / endopeptidase activity / ubiquitin-dependent protein catabolic process / proteolysis ...proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / endopeptidase activity / ubiquitin-dependent protein catabolic process / proteolysis / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) / Trypanosoma brucei brucei (eukaryote) | |||||||||
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_20879.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-20879-v30.xml emd-20879.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
Images | emd_20879.png | 84.4 KB | ||
Filedesc metadata | emd-20879.cif.gz | 5.6 KB | ||
Others | emd_20879_additional.map.gz emd_20879_half_map_1.map.gz emd_20879_half_map_2.map.gz | 62.8 MB 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20879 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20879 | HTTPS FTP |
-Validation report
Summary document | emd_20879_validation.pdf.gz | 928.7 KB | Display | EMDB validaton report |
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Full document | emd_20879_full_validation.pdf.gz | 928.3 KB | Display | |
Data in XML | emd_20879_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | emd_20879_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20879 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20879 | HTTPS FTP |
-Related structure data
Related structure data | 6uthMC 6utfC 6utgC 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_20879.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 20S proteasome, 20S proteasome singly capped with a PA26/E102A_PANc, together with LFP incubation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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_20879_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_20879_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_20879_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Singly capped T20S proteasome by PA26PANc, LFP
Entire | Name: Singly capped T20S proteasome by PA26PANc, LFP |
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Components |
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-Supramolecule #1: Singly capped T20S proteasome by PA26PANc, LFP
Supramolecule | Name: Singly capped T20S proteasome by PA26PANc, LFP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
-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: 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 #2: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 22.294848 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: TTTVGITLKD AVIMATERRV TMENFIMHKN GKKLFQIDTY TGMTIAGLVG DAQVLVRYMK AELELYRLQR RVNMPIEAVA TLLSNMLNQ VKYMPYMVQL LVGGIDTAPH VFSIDAAGGS VEDIYASTGS GSPFVYGVLE SQYSEKMTVD EGVDLVIRAI S AAKQRDSA ...String: TTTVGITLKD AVIMATERRV TMENFIMHKN GKKLFQIDTY TGMTIAGLVG DAQVLVRYMK AELELYRLQR RVNMPIEAVA TLLSNMLNQ VKYMPYMVQL LVGGIDTAPH VFSIDAAGGS VEDIYASTGS GSPFVYGVLE SQYSEKMTVD EGVDLVIRAI S AAKQRDSA SGGMIDVAVI TRKDGYVQLP TDQIESRIRK LGLIL UniProtKB: Proteasome subunit beta |
-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: 25.125619 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: AYDRAITVFS PDGRLFQVEY AREAVKKGST ALGMKFANGV LLISDKKVRS RLIEQNSIEK IQLIDDYVAA VTSGLVADAR VLVDFARIS AQQEKVTYGS LVNIENLVKR VADQMQQYTQ YGGVRPYGVS LIFAGIDQIG PRLFDCDPAG TINEYKATAI G SGKDAVVS ...String: AYDRAITVFS PDGRLFQVEY AREAVKKGST 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 |
-Macromolecule #4: Proteasome activator protein PA26
Macromolecule | Name: Proteasome activator protein PA26 / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) |
Molecular weight | Theoretical: 25.088582 KDa |
Recombinant expression | Organism: Escherichia phage EcSzw-2 (virus) |
Sequence | String: KRAALIQNLR DSYTETSSFA VIEEWAAGTL QEIEGIAKAA VEAHGTIRNS TYGRAQAEKS PEQLLGVLQR YQDLCHNVYC QAETIRTVI AIRIPEHKEA DNLGVAVQHA VLKVIDELEI KTLGSGEKSG SGGAPTPIGM YALREYLSAR STVEDKLLGS V DAESGKTK ...String: KRAALIQNLR DSYTETSSFA VIEEWAAGTL QEIEGIAKAA VEAHGTIRNS TYGRAQAEKS PEQLLGVLQR YQDLCHNVYC QAETIRTVI AIRIPEHKEA DNLGVAVQHA VLKVIDELEI KTLGSGEKSG SGGAPTPIGM YALREYLSAR STVEDKLLGS V DAESGKTK GGSQSPSLLL ELRQIDADFM LKVELATTHL STMVRAVINA YLLNWKKLIQ PRGGHLDVLY R UniProtKB: Proteasome activator protein PA26 |
-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 TALOS ARCTICA |
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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: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / 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: 55000 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |