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- EMDB-20878: Allosteric coupling between alpha-rings of the 20S proteasome, 20... -

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Basic information

Entry
Database: EMDB / ID: EMD-20878
TitleAllosteric coupling between alpha-rings of the 20S proteasome, 20S singly capped with a PA26/V230F
Map dataAllosteric coupling between alpha-rings of the 20S proteasome, 20S singly capped with a PA26/V230F
Sample
  • Complex: The complex of Archaea 20S singly capped by one PA26/V230F
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome activator protein PA26
    • Protein or peptide: Proteasome subunit alpha
Keywordsproteasome / PA26/V230F / singly-capped / HYDROLASE
Function / homology
Function and homology information


proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature ...Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha / Proteasome subunit beta / Proteasome activator protein PA26
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic) / Trypanosoma brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYu Z / Cheng Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM082893 United States
CitationJournal: 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
DepositionOct 29, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseSep 9, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.472
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.472
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6utg
  • Surface level: 0.472
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20878.png

Downloads & links

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Map

FileDownload / File: emd_20878.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAllosteric coupling between alpha-rings of the 20S proteasome, 20S singly capped with a PA26/V230F
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 320 pix.
= 394.88 Å		1.23 Å/pix.
x 320 pix.
= 394.88 Å		1.23 Å/pix.
x 320 pix.
= 394.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.234 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.472 / Movie #1: 0.472
Minimum - Maximum-2.11635 - 3.312607
Average (Standard dev.)-0.00021744032 (±0.113970034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 394.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2341.2341.234
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z394.880394.880394.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ428428428
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.1163.313-0.000

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Supplemental data

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Additional map: #1

Fileemd_20878_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_20878_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_20878_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of Archaea 20S singly capped by one PA26/V230F

EntireName: The complex of Archaea 20S singly capped by one PA26/V230F
Components
  • Complex: The complex of Archaea 20S singly capped by one PA26/V230F
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome activator protein PA26
    • Protein or peptide: Proteasome subunit alpha

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Supramolecule #1: The complex of Archaea 20S singly capped by one PA26/V230F

SupramoleculeName: The complex of Archaea 20S singly capped by one PA26/V230F
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)

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Macromolecule #1: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightTheoretical: 22.294848 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: 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

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Macromolecule #2: Proteasome subunit alpha

MacromoleculeName: Proteasome subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightTheoretical: 25.125619 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: 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

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Macromolecule #3: Proteasome activator protein PA26

MacromoleculeName: Proteasome activator protein PA26 / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 24.995404 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: KRAALIQNLR DSYTETSSFA VIEEWAAGTL QEIEGIAKAA AEAHGVIRNS TYGRAQAEKS PEQLLGVLQR YQDLCHNVYC QAETIRTVI AIRIPEHKEE DNLGVAVQHA VLKIIDELEI KTLGSGEKSG SGGAPTPIGM YALREYLSAR STVEDKLLGS V DAESGKTK ...String:
KRAALIQNLR DSYTETSSFA VIEEWAAGTL QEIEGIAKAA AEAHGVIRNS TYGRAQAEKS PEQLLGVLQR YQDLCHNVYC QAETIRTVI AIRIPEHKEE DNLGVAVQHA VLKIIDELEI KTLGSGEKSG SGGAPTPIGM YALREYLSAR STVEDKLLGS V DAESGKTK GGSQSPSLLL ELRQIDADFM LKVELATTHL STMVRAVINA YLLNWKKLIQ PRTGTDHMFS

UniProtKB: Proteasome activator protein PA26

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Macromolecule #4: Proteasome subunit alpha

MacromoleculeName: Proteasome subunit alpha / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightTheoretical: 24.718178 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: RAITVFSPDG RLFQVEYARE AVKKGSTALG MKFANGVLLI SDKKVRSRLI EQNSIEAIQL IDDYVAAVTS GLVADARVLV DFARISAQQ EKVTYGSLVN IENLVKRVAD QMQQYTQYGG VRPYGVSLIF AGIDQIGPRL FDCDPAGTIN EYKATAIGSG K DAVVSFLE ...String:
RAITVFSPDG RLFQVEYARE AVKKGSTALG MKFANGVLLI SDKKVRSRLI EQNSIEAIQL IDDYVAAVTS GLVADARVLV DFARISAQQ EKVTYGSLVN IENLVKRVAD QMQQYTQYGG VRPYGVSLIF AGIDQIGPRL FDCDPAGTIN EYKATAIGSG K DAVVSFLE REYKENLPEK EAVTLGIKAL KSSLEEGEEL KAPEIASITV GNKYRIYDQE EVKKFL

UniProtKB: Proteasome subunit alpha

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ipm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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