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- PDB-9qoo: Composite model: Ternary complex of the human 20S proteasome in c... -

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Entry
Database: PDB / ID: 9qoo
TitleComposite model: Ternary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2
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 / histone chaperone activity / nuclear protein quality control by the ubiquitin-proteasome system / positive regulation of adaptive immune response / purine ribonucleoside triphosphate binding / embryo development ending in birth or egg hatching / positive regulation of innate immune response / Regulation of ornithine decarboxylase (ODC) ...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 / purine ribonucleoside triphosphate binding / embryo development ending in birth or egg hatching / positive regulation of innate immune response / Regulation of ornithine decarboxylase (ODC) / nuclear import signal receptor activity / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome core complex, alpha-subunit complex / transcription repressor complex / proteasome complex / : / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / transcription coregulator activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / negative regulation of inflammatory response to antigenic stimulus / Degradation of DVL / P-body / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / 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 / cerebral cortex development / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / positive regulation of interleukin-6 production / small GTPase binding / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / response to virus / FCERI mediated NF-kB activation / nuclear matrix / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / protein import into nucleus / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / UCH proteinases / KEAP1-NFE2L2 pathway / nuclear envelope / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / secretory granule lumen / endopeptidase activity / histone binding / response to lipopolysaccharide / protein-macromolecule adaptor activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium
Similarity search - Function
: / 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 / Proteasome subunit alpha 1 / Proteasome subunit alpha5 / Proteasome subunit alpha6 ...: / 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 / 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: 3.3 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: To Be Published
Title: A multivalent adaptor mechanism drives the nuclear import of proteasomes
Authors: Brunner, H. / Kalis, R.W. / Grundmann, L. / Hodakova, Z. / Koskova, Z. / Grishkovskaya, I. / de Almeida, M. / Hinterndorfer, M. / Hoefflin, S. / Andersch, F. / Kotisch, H. / Dickmanns, A. / ...Authors: Brunner, H. / Kalis, R.W. / 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 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
I: Akirin-2
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)401,48112
Polymers401,48112
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, 5 molecules ABCDI

#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
Details: ...Details: MGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKTAGLEVLFQGPAAAAAAGAASGLPGPVAQGLKEALVDTLTGILSPVQEVRAAAEEQIKVLEVTEEFGVHLAELTVDPQGALAIRQLASVILKQYVETHWCAQSEKFRPPETTERAKIVIRELLPNGLRESISKVRSSVAYAVSAIAHWDWPEAWPQLFNLLMEMLVSGDLNAVHGAMRVLTEFTREVTDTQMPLVAPVILPEMYKIFTMAEVYGIRTRSRAVEIFTTCAHMICNMEELEKGAAKVLIFPVVQQFTEAFVQALQIPDGPTSDSGFKMEVLKAVTALVKNFPKHMVSSMQQILPIVWNTLTESAAFYVRTEVNYTEEVEDPVDSDGEVLGFENLVFSIFEFVHALLENSKFKSTVKKALPELIYYIILYMQITEEQIKVWTANPQQFVEDEDDDTFSYTVRIAAQDLLLAVATDFQNESAAALAAAATRHLQEAEQTKNSGTEHWWKIHEACMLALGSVKAIITDSVKNGRIHFDMHGFLTNVILADLNLSVSPFLLGRALWAASRFTVAMSPELIQQFLQATVSGLHETQPPSVRISAVRAIWGYCDQLKVSESTHVLQPFLPSILDGLIHLAAQFSSEVLNLVMETLCIVCTVDPEFTASMESKICPFTIAIFLKYSNDPVVASLAQDIFKELSQIEACQGPMQMRLIPTLVSIMQAPADKIPAGLCATAIDILTTVVRNTKPPLSQLLICQAFPAVAQCTLHTDDNATMQNGGECLRAYVSVTLEQVAQWHDEQGHNGLWYVMQVVSQLLDPRTSEFTAAFVGRLVSTLISKAGRELGENLDQILRAILSKMQQAETLSVMQSLIMVFAHLVHTQLEPLLEFLCSLPGPTGKPALEFVMAEWTSRQHLFYGQYEGKVSSVALCKLLQHGINADDKRLQDIRVKGEEIYSMDEGIRTRSKSAKNPERWTNIPLLVKILKLIINELSNVMEANAARQATPAEWSQDDSNDMWEDQEEEEEEEEDGLAGQLLSDILATSKYEEDYYEDDEEDDPDALKDPLYQIDLQAYLTDFLCQFAQQPCYIMFSGHLNDNERRVLQTIGI
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.: 4
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

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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: 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 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
1crYOLOparticle selection
2EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61740 / Symmetry type: POINT

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