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- PDB-6he7: 20S proteasome from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 6he7
Title20S proteasome from Archaeoglobus fulgidus
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE / PAN / Proteasome / AAA-ATPase / Archaea
Function / homology
Function and homology information


proteasome core complex, beta-subunit complex / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / cytoplasm
Proteasome alpha subunit, archaeal / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome subunit / Nucleophile aminohydrolases, N-terminal / Proteasome B-type subunit / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / Proteasome, subunit alpha/beta / Proteasome beta-type subunit, conserved site / Proteasome alpha-type subunit ...Proteasome alpha subunit, archaeal / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome subunit / Nucleophile aminohydrolases, N-terminal / Proteasome B-type subunit / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / Proteasome, subunit alpha/beta / Proteasome beta-type subunit, conserved site / Proteasome alpha-type subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 4-Layer Sandwich / Alpha Beta
Proteasome subunit alpha / Proteasome subunit beta
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsMajumder, P. / Rudack, T. / Beck, F. / Baumeister, W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle.
Authors: Parijat Majumder / Till Rudack / Florian Beck / Radostin Danev / Günter Pfeifer / István Nagy / Wolfgang Baumeister /
Abstract: Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein ...Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein homeostasis, and control vital cellular processes. While the eukaryotic 26S proteasome is extensively characterized, its putative evolutionary precursor, the archaeal proteasome, remains poorly understood. The primordial archaeal proteasome consists of a 20S proteolytic core particle (CP), and an AAA-ATPase module. This minimal complex degrades protein unassisted by non-ATPase subunits that are present in a 26S proteasome regulatory particle (RP). Using cryo-EM single-particle analysis, we determined structures of the archaeal CP in complex with the AAA-ATPase PAN (proteasome-activating nucleotidase). Five conformational states were identified, elucidating the functional cycle of PAN, and its interaction with the CP. Coexisting nucleotide states, and correlated intersubunit signaling features, coordinate rotation of the PAN-ATPase staircase, and allosterically regulate N-domain motions and CP gate opening. These findings reveal the structural basis for a sequential around-the-ring ATPase cycle, which is likely conserved in AAA-ATPases.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

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Assembly

Deposited unit
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
1: Proteasome subunit beta
2: Proteasome subunit beta
3: Proteasome subunit beta
4: Proteasome subunit beta
5: Proteasome subunit beta
6: Proteasome subunit beta
7: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)339,25914
Polymers339,25914
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area45310 Å2
ΔGint-146 kcal/mol
Surface area106950 Å2
MethodPISA

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Components

#1: Protein
Proteasome subunit alpha / / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 26333.248 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: psmA, AF_0490 / Production host: Escherichia coli (E. coli)
References: UniProt: O29760, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 22132.283 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: psmB, AF_0481 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P996, 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: 20S proteasomeProteasome / Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 0.710 MDa / Experimental value: NO
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4MotionCorr2CTF correction
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105384 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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