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

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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: Nat Commun / Year: 2026
Title: A multivalent adaptor mechanism drives the nuclear import of proteasomes.
Authors: Hanna L Brunner / Robert W Kalis / Lorenz Grundmann / Zuzana Hodáková / Zuzana Koskova / Irina Grishkovskaya / Melanie de Almeida / Matthias Hinterndorfer / Hannah Knaudt / Simon Höfflin ...Authors: Hanna L Brunner / Robert W Kalis / Lorenz Grundmann / Zuzana Hodáková / Zuzana Koskova / Irina Grishkovskaya / Melanie de Almeida / Matthias Hinterndorfer / Hannah Knaudt / Simon Höfflin / Florian Andersch / Harald Kotisch / Achim Dickmanns / Sara Cuylen-Haering / Johannes Zuber / David Haselbach /
Abstract: Nuclear protein homeostasis, including transcription factor turnover, critically depends on the nuclear proteasomes that must be imported after cell division. This dynamic process requires AKIRIN2, a ...Nuclear protein homeostasis, including transcription factor turnover, critically depends on the nuclear proteasomes that must be imported after cell division. This dynamic process requires AKIRIN2, a small unstructured protein whose mechanistic role has remained elusive despite its essential function. Using an integrated approach combining protein-wide saturation mutagenesis screens, cryo-EM, and biochemical reconstitution, we characterize AKIRIN2 as a scaffold protein that coordinates the assembly of an importin cluster around the proteasome. AKIRIN2 binds in multiple copies to the 20S proteasome and simultaneously interacts with importin IPO9 and the KPNA2/KPNB1 heterodimer. In the nucleus, RanGTP triggers importin dissociation, releasing the proteasome, while AKIRIN2 undergoes ubiquitin-independent degradation. Our findings reveal how AKIRIN2's multivalency facilitates the recruitment of multiple importins to the proteasome, a critical adaptation for transporting this large macromolecular complex into the nucleus and maintaining the nuclear proteome.
History
DepositionMar 25, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 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
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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

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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
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AxesZYX

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Half map: #1

Fileemd_53246_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53246_half_map_2.map
Projections & Slices
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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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