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- EMDB-54521: Structure of the Pyrococcus abyssi 20S proteasome bound to the ar... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54521
TitleStructure of the Pyrococcus abyssi 20S proteasome bound to the archaeal activator APA1
Map dataEnsemble view of the 20S proteasome from Pyrococcus abyssi and the capping protein Q9UYJ3 (APA1)
Sample
  • Cell: 20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3)
    • Complex: 20S Proteasome from P. abyssi
      • Protein or peptide: Proteasome subunit alpha
    • Complex: Archaeal proteasome activator 1
      • Protein or peptide: Archaeal proteasome activator 1
KeywordsComplex Proteasome Archaea Proteasome activator / PROTEIN BINDING
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMusso F / Marino Puertas L / Weis F / Schoehn G / Franzetti B
Funding support France, 1 items
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, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54521.png

Downloads & links

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Map

FileDownload / File: emd_54521.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnsemble view of the 20S proteasome from Pyrococcus abyssi and the capping protein Q9UYJ3 (APA1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 480 pix.
= 549.6 Å		1.15 Å/pix.
x 480 pix.
= 549.6 Å		1.15 Å/pix.
x 480 pix.
= 549.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.7140532 - 7.0689178
Average (Standard dev.)0.03675891 (±0.13032712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 549.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 20S Proteasome from P. abyssi in complex with the heptameric prot...

EntireName: 20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3)
Components
  • Cell: 20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3)
    • Complex: 20S Proteasome from P. abyssi
      • Protein or peptide: Proteasome subunit alpha
    • Complex: Archaeal proteasome activator 1
      • Protein or peptide: Archaeal proteasome activator 1

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Supramolecule #1: 20S Proteasome from P. abyssi in complex with the heptameric prot...

SupramoleculeName: 20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3)
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Assembled 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 ...Details: Assembled 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.
Source (natural)Organism: Pyrococcus abyssi (archaea)

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Supramolecule #2: 20S Proteasome from P. abyssi

SupramoleculeName: 20S Proteasome from P. abyssi / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 711 KDa

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Supramolecule #3: Archaeal proteasome activator 1

SupramoleculeName: Archaeal proteasome activator 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Details: Heptameric form of the protein, in complex with the proteasome. No tags.
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 234 KDa

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Macromolecule #1: Archaeal proteasome activator 1

MacromoleculeName: Archaeal proteasome activator 1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 33.512344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKASKLAVKL LKTENDEIIY YDPIYHGRTL KVIGIDDDPA LVMEYLLAQY KEKGYNVIVF DTSGKFPTSL FDNILRIEEN SPAGLDPLK LARVGLIKDP YSAVTIIQTI YELDRASTEK LYADFIKGKV NSMDEVVRSK ESYAEVINES YTELDEMLFS G EPMKVPES ...String:
MKASKLAVKL LKTENDEIIY YDPIYHGRTL KVIGIDDDPA LVMEYLLAQY KEKGYNVIVF DTSGKFPTSL FDNILRIEEN SPAGLDPLK LARVGLIKDP YSAVTIIQTI YELDRASTEK LYADFIKGKV NSMDEVVRSK ESYAEVINES YTELDEMLFS G EPMKVPES CLIDLSALNS ITLTGNAFLI LAAMLEDRRS VAYGLYDVSV LTFTDSGNAG LPLITRAARK RVSIVGTRYA LD QILNIPG PTLLLYNDPD VQSAIYESQG VPQGFRRFVE KGEGAYIVRS PETIEVEFGM LLR

UniProtKB: Uncharacterized protein

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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
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 29.035293 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAFVPPQAGY DRAITVFSPD GRLFQVNYAR EAVKRGATAV GVKCKDGVVL AVEKRITSRL IEPESYEKIF QIDDHIAAAS SGIIADARV LVNRARLEAQ IHRLTYGEPA PLAVIVKKIC DLKQMHTQYG GVRPFGAALL MAGVNDKPEL YETDPSGAYF A WKAVAIGS ...String:
MAFVPPQAGY DRAITVFSPD GRLFQVNYAR EAVKRGATAV GVKCKDGVVL AVEKRITSRL IEPESYEKIF QIDDHIAAAS SGIIADARV LVNRARLEAQ IHRLTYGEPA PLAVIVKKIC DLKQMHTQYG GVRPFGAALL MAGVNDKPEL YETDPSGAYF A WKAVAIGS GRNTAMAIFE DKYRDDMTLD EAIKLAIFAL AKTMEKPSAE NIEVAVITVK DKKFRKLSKE EIEKFLGEVM KE VEEEEVK EKEEDYSELD SHY

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: 8
Details: 50 mM Tris pH 8.0, 150 mM NaCl, 150 mM KCl, 10 mM MgCl2
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsSEC-pure form of the 20S

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4835 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 534489
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Reconstruction from Ab-initio volumes generated from 2D projections.
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5)
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.
Number images used: 50092
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5
Details: During a final round of Heterogeneous refinement, input volumes containing a good preliminary homogeneous refinement of the whole complex, APA1 alone, 20S alone and duplicate particles were ...Details: During a final round of Heterogeneous refinement, input volumes containing a good preliminary homogeneous refinement of the whole complex, APA1 alone, 20S alone and duplicate particles were submitted and forced to undergo hard classification

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: Other, initial_model_type: experimental modelXray structure solved in our lab for APA1
source_name: AlphaFold, initial_model_type: in silico modelSingle chain model used, copies created with local EM fitting tool in ChimeraX

2-f1

DetailsModel 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation
Output model

PDB-9s34:
Structure of the Pyrococcus abyssi 20S proteasome alpha subunit bound to the capping protein APA1

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