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- PDB-9qon: Ternary complex of the human 20S proteasome in complex with Impor... -

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Entry
Database: PDB / ID: 9qon
TitleTernary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 - focussed refinement on the alpha subunits, Ipo-9 and Ak2
Components
  • (Proteasome subunit alpha type- ...) x 7
  • Akirin-2
  • Importin-9
KeywordsPROTEIN TRANSPORT / 20S proteasome / 20S / proteasome / nuclear iport / akirin / akirin2 / importin 9 / importin
Function / homology
Function and homology information


proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / nuclear protein quality control by the ubiquitin-proteasome system / histone chaperone activity / positive regulation of adaptive immune response / embryo development ending in birth or egg hatching / positive regulation of innate immune response / purine ribonucleoside triphosphate binding / CD8-positive, alpha-beta T cell differentiation ...proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / nuclear protein quality control by the ubiquitin-proteasome system / histone chaperone activity / positive regulation of adaptive immune response / embryo development ending in birth or egg hatching / positive regulation of innate immune response / purine ribonucleoside triphosphate binding / CD8-positive, alpha-beta T cell differentiation / CD8-positive, alpha-beta T cell homeostasis / thymic T cell selection / Antigen processing: Ub, ATP-independent proteasomal degradation / structural constituent of proteasome / spermatoproteasome complex / nuclear import signal receptor activity / negative regulation of regulatory T cell differentiation / T-helper 1 cell differentiation / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Proteasome assembly / cellular response to type I interferon / T-helper 17 cell differentiation / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / flagellated sperm motility / sperm end piece / immune system process / myofibril / proteasomal ubiquitin-independent protein catabolic process / ciliary tip / NF-kappaB binding / proteasome core complex, alpha-subunit complex / regulation of G1/S transition of mitotic cell cycle / positive regulation of interleukin-2 production / transcription repressor complex / proteasome storage granule / response to type II interferon / proteasome complex / protein import into nucleus / regulation of proteasomal protein catabolic process / meiotic cell cycle / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / negative regulation of inflammatory response to antigenic stimulus / proteasomal protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / lipopolysaccharide binding / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / positive regulation of type II interferon production / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / P-body / TNFR2 non-canonical NF-kB pathway / protein catabolic process / cerebral cortex development / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / positive regulation of interleukin-6 production / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / response to virus / Negative regulation of NOTCH4 signaling / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / adaptive immune response / CDK-mediated phosphorylation and removal of Cdc6 / small GTPase binding / ABC-family protein mediated transport / CLEC7A (Dectin-1) signaling / transcription coregulator activity / Activation of STAT3 by cadherin engagement / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / nuclear matrix
Similarity search - Function
: / Importin-9 central HEAT repeats / : / Importin-11-like, TPR repeats / Akirin / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Proteasome subunit alpha 1 ...: / Importin-9 central HEAT repeats / : / Importin-11-like, TPR repeats / Akirin / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Proteasome subunit alpha 1 / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunit, conserved site / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit alpha type-6 / Akirin-2 / Importin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
A: Importin-9
B: Akirin-2
C: Akirin-2
D: Akirin-2
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1


Theoretical massNumber of molelcules
Total (without water)378,95611
Polymers378,95611
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

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Protein , 2 types, 4 molecules ABCD

#1: 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) / Strain (production host): Arctic Express / References: UniProt: Q96P70
#2: Protein Akirin-2


Mass: 22525.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKIRIN2, C6orf166 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53H80

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Proteasome subunit alpha type- ... , 7 types, 7 molecules FGOPQRS

#3: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25788
#4: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA6, PROS27 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60900
#5: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA2, HC3, PSC3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25787
#6: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA4, HC9, PSC9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25789
#7: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA7, HSPC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14818
#8: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28066
#9: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29595.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA1, HC2, NU, PROS30, PSC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25786

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Details

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: #2-#9, #1 / 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 type: Quantifoil R3.5/1
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: 1900 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 44.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61740 / Symmetry type: POINT

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