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- PDB-6utg: Allosteric coupling between alpha-rings of the 20S proteasome, 20... -

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Basic information

Entry
Database: PDB / ID: 6utg
TitleAllosteric coupling between alpha-rings of the 20S proteasome, 20S singly capped with a PA26/V230F
Components
  • (Proteasome subunit alpha) x 2
  • Proteasome activator protein PA26
  • Proteasome subunit beta
KeywordsHYDROLASE / proteasome / PA26/V230F / singly-capped
Function / homology
Function and homology information


proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis / cytoplasm
Proteasome, subunit alpha/beta / Proteasome activator PA28, C-terminal domain / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator superfamily / Nucleophile aminohydrolases, N-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasome beta-type subunit, conserved site ...Proteasome, subunit alpha/beta / Proteasome activator PA28, C-terminal domain / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator superfamily / Nucleophile aminohydrolases, N-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasome beta-type subunit, conserved site / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain
Proteasome subunit alpha / Proteasome subunit beta / Proteasome activator protein PA26
Biological speciesThermoplasma acidophilum (acidophilic)
Trypanosoma brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYu, Z. / Cheng, Y.
Funding support United States, 1items
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
1: Proteasome subunit beta
2: Proteasome subunit beta
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome activator protein PA26
P: Proteasome activator protein PA26
Q: Proteasome activator protein PA26
R: Proteasome activator protein PA26
S: Proteasome activator protein PA26
T: Proteasome activator protein PA26
U: Proteasome activator protein PA26
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit alpha
b: Proteasome subunit alpha
c: Proteasome subunit alpha
d: Proteasome subunit alpha
e: Proteasome subunit alpha
f: Proteasome subunit alpha
g: Proteasome subunit alpha


Theoretical massNumber of molelcules
Total (without water)836,00235
Polymers836,00235
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area139580 Å2
ΔGint-477 kcal/mol
Surface area261690 Å2

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Components

#1: Protein
Proteasome subunit beta / / 20S proteasome subunit B / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 22294.848 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmB, Ta0612 / Production host: Escherichia phage EcSzw-2 (bacteriophage)
References: UniProt: P28061, proteasome endopeptidase complex
#2: Protein
Proteasome subunit alpha / / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 25125.619 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Production host: Escherichia phage EcSzw-2 (bacteriophage)
References: UniProt: P25156, proteasome endopeptidase complex
#3: Protein
Proteasome activator protein PA26


Mass: 24995.404 Da / Num. of mol.: 7 / Mutation: V230F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia phage EcSzw-2 (bacteriophage) / References: UniProt: Q9U8G2
#4: Protein
Proteasome subunit alpha / / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 24718.178 Da / Num. of mol.: 7 / Mutation: K66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Production host: Escherichia phage EcSzw-2 (bacteriophage)
References: UniProt: P25156, proteasome endopeptidase complex

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complex of Archaea 20S singly capped by one PA26/V230F
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Source (recombinant)Organism: Escherichia phage EcSzw-2 (bacteriophage)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50000 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00958912
ELECTRON MICROSCOPYf_angle_d1.14979541
ELECTRON MICROSCOPYf_dihedral_angle_d4.99136015
ELECTRON MICROSCOPYf_chiral_restr0.0669310
ELECTRON MICROSCOPYf_plane_restr0.00710206

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