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- EMDB-53246: Consensus refinement: Ternary complex of the human 20S proteasome... -

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Basic information

Entry
Database: EMDB / ID: EMD-53246
TitleConsensus refinement: Ternary complex of the human 20S proteasome in complex with Importin-9 and two homo dimers of Akirin-2. Focussed refinement
Map dataNon-postprocessed map
Sample
  • Complex: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
Keywords20S proteasome / 20S / proteasome / nuclear iport / akirin / akirin2 / importin 9 / importin / PROTEIN TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBrunner HL / Grundmann L / Haslelbach D
Funding supportEuropean Union, Austria, 2 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission847548European Union
Austrian Science Fund10.55776/F79 Austria
CitationJournal: To Be Published
Title: A multivalent adaptor mechanism drives the nuclear import of proteasomes
Authors: Brunner H / Kalis RW / Grundmann L / Hodakova Z / Koskova Z / Grishkovskaya I / de Almeida M / Hinterndorfer M / Hoefflin S / Andersch F / Kotisch H / Dickmanns A / Cuylen-Haering S / Zuber J / Haselbach D
History
DepositionMar 25, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53246.png

Downloads & links

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Map

FileDownload / File: emd_53246.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 300 pix.
= 429. Å		1.43 Å/pix.
x 300 pix.
= 429. Å		1.43 Å/pix.
x 300 pix.
= 429. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.386
Minimum - Maximum-0.8082995 - 1.7091472
Average (Standard dev.)-0.0018602354 (±0.04644024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 428.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53246_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53246_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_53246_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 : Ternary complex of the human 20S proteasome in complex with two d...

EntireName: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
Components
  • Complex: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9

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Supramolecule #1: Ternary complex of the human 20S proteasome in complex with two d...

SupramoleculeName: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)

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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: 7.5
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61740
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: RELION (ver. 5.0) / Software - details: T=100, without image alignment
FSC plot (resolution estimation)

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