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- EMDB-54518: Focused map of the 20S proteasome from Pyrococcus abyssi in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-54518
TitleFocused map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (APA1)
Map dataUnprocessed focused map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (APA1)
Sample
  • Cell: 20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3)
    • Complex: 20S Proteasome from P. abyssi
KeywordsComplex Proteasome Archaea Proteasome activator / PROTEIN BINDING
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: Focused map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (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_54518.png

Downloads & links

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Map

FileDownload / File: emd_54518.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnprocessed focused map of the 20S proteasome from Pyrococcus abyssi in complex with 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: 0.26
Minimum - Maximum-0.5848336 - 1.1900442
Average (Standard dev.)0.00019446237 (±0.025616085)
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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Additional map: sharpened map used for model building

Fileemd_54518_additional_1.map
Annotationsharpened map used for model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54518_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54518_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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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: #1-#2
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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

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) / 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
FSC plot (resolution estimation)

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

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