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- PDB-9qop: Binary complex of human Importin-9 with one homodimer of Akirin-2 -

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Basic information

Entry
Database: PDB / ID: 9qop
TitleBinary complex of human Importin-9 with one homodimer of Akirin-2
Components
  • Akirin-2
  • Importin-9
KeywordsPROTEIN TRANSPORT / 20S proteasome / 20S / proteasome / nuclear import / akirin / akirin2 / importin 9 / importin
Function / homology
Function and homology information


proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / histone chaperone activity / nuclear protein quality control by the ubiquitin-proteasome system / positive regulation of adaptive immune response / embryo development ending in birth or egg hatching / positive regulation of innate immune response / nuclear import signal receptor activity / transcription repressor complex ...proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / histone chaperone activity / nuclear protein quality control by the ubiquitin-proteasome system / positive regulation of adaptive immune response / embryo development ending in birth or egg hatching / positive regulation of innate immune response / nuclear import signal receptor activity / transcription repressor complex / transcription coregulator activity / cerebral cortex development / positive regulation of interleukin-6 production / small GTPase binding / protein import into nucleus / nuclear envelope / histone binding / response to lipopolysaccharide / protein-macromolecule adaptor activity / adaptive immune response / defense response to bacterium / innate immune response / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Importin-11-like, TPR repeats / : / Importin-9 central HEAT repeats / Akirin / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Akirin-2 / Importin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBrunner, H.L. / Grundmann, L. / David, H.
Funding supportEuropean Union, Austria, 2items
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 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Akirin-2
A: Importin-9
C: Akirin-2


Theoretical massNumber of molelcules
Total (without water)161,1133
Polymers161,1133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Akirin-2


Mass: 22525.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKIRIN2, C6orf166 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE / References: UniProt: Q53H80
#2: Protein Importin-9 / Imp9 / Ran-binding protein 9 / RanBP9


Mass: 116062.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPO9, IMP9, KIAA1192, RANBP9, HSPC273 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96P70
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

ComponentName: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 360044 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044325
ELECTRON MICROSCOPYf_angle_d0.4955394
ELECTRON MICROSCOPYf_dihedral_angle_d5.4521076
ELECTRON MICROSCOPYf_chiral_restr00
ELECTRON MICROSCOPYf_plane_restr0.0041076

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