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- PDB-9s34: Structure of the Pyrococcus abyssi 20S proteasome alpha subunit b... -

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Basic information

Entry
Database: PDB / ID: 9s34
TitleStructure of the Pyrococcus abyssi 20S proteasome alpha subunit bound to the capping protein APA1
Components
  • Archaeal proteasome activator 1
  • Proteasome subunit alpha
KeywordsPROTEIN BINDING / Complex Proteasome Archaea Proteasome activator
Function / homology
Function and homology information


threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
Proteasome alpha subunit, archaeal / 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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Uncharacterized protein / Proteasome subunit alpha
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMusso, F. / Marino Puertas, L. / Weis, F. / Schoehn, G. / Franzetti, B.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Structure of the Pyrococcus abyssi 20S proteasome alpha subunit bound to the capping protein APA1
Authors: Musso, F. / Marino Puertas, L. / Girard, E. / Gabel, F. / Coute, Y. / Flament, D. / Chenavier, F. / Weis, F. / Schoehn, G. / Franzetti, B.
History
DepositionJul 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaeal proteasome activator 1
B: Archaeal proteasome activator 1
C: Archaeal proteasome activator 1
D: Archaeal proteasome activator 1
E: Archaeal proteasome activator 1
F: Archaeal proteasome activator 1
G: Archaeal proteasome activator 1
H: Proteasome subunit alpha
N: Proteasome subunit alpha
I: Proteasome subunit alpha
J: Proteasome subunit alpha
K: Proteasome subunit alpha
L: Proteasome subunit alpha
M: Proteasome subunit alpha


Theoretical massNumber of molelcules
Total (without water)437,83314
Polymers437,83314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, gel filtration, surface plasmon resonance, Actually BioLayer interferometry, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Archaeal proteasome activator 1


Mass: 33512.344 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: PAB1363 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UYJ3
#2: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 29035.293 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: psmA, PYRAB06070, PAB0417 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V122
Has protein modificationN

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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

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
120S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3)CELLAssembled 20S core particle reconstituted in vitro from recombinant expression of its three subunit types: alpha, beta-1, beta-2. Beta 2 subunit bears an N-terminal His-tag. Capping protein APA1 sitting on the outer Alpha ring.all0RECOMBINANT
220S Proteasome from P. abyssiCOMPLEX#21RECOMBINANT
3Archaeal proteasome activator 1COMPLEXHeptameric form of the protein, in complex with the proteasome. No tags.#11RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11
220.711 MDaYES
330.234 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Pyrococcus abyssi (archaea)29292
32Pyrococcus abyssi (archaea)29292
43Pyrococcus abyssi (archaea)29292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 8
Details: 50 mM Tris pH 8.0, 150 mM NaCl, 150 mM KCl, 10 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: SEC-pure form of the 20S
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4835

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2SerialEMimage acquisition
7UCSF ChimeraX1.8model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC4.53D reconstruction
13PHENIX1.21.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 534489
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50092
Details: 50,092 particles aligning to the complex were used for Non Uniform refinement with an imposed C7 symmetry. This yielded the consensus alignment at 3.23 Angstrom, which served as a base for ...Details: 50,092 particles aligning to the complex were used for Non Uniform refinement with an imposed C7 symmetry. This yielded the consensus alignment at 3.23 Angstrom, which served as a base for the focused refinements used to make this composite map. Upon reconstruction with imposed C7 symmetry, the two proteasome Beta1-2 subunits of the 20S became merged together. We noticed that the same was happening when the 20S proteasome was reconstructed without an imposed symmetry, suggesting a random distribution of the two subunit types in the Beta rings. Due to the high degree of similarity between the two proteins (>70 percent sequence identity) and the small number of particles, we opted for not continuing with further 3D classification.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross correlation
Details: Model building done in coot, refinement in Phenix. No models built for the merged Beta 1-2 chains of the 20S proteasome, due to the identical folding of the two proteins and the very small ...Details: Model building done in coot, refinement in Phenix. No models built for the merged Beta 1-2 chains of the 20S proteasome, due to the identical folding of the two proteins and the very small (single side chains) differences between the two subunits, which prevented effective 3D classification with the small number of particles left. IMPORTANT: the outlier Y204 nonplanar bond was modelled as such based on a higher resolution X-ray model, to be deposited soon.
Atomic model building
ID 3D fitting-IDDetails (eV)Source nameTypeAccession codeInitial refinement model-ID
11Xray structure solved in our lab for APA1Otherexperimental model
21Single chain model used, copies created with local EM fitting tool in ChimeraXAlphaFoldin silico modelAF-Q9V122-F12

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