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- EMDB-53266: Binary complex of human Importin-9 with one homodimer of Akirin-2 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53266
TitleBinary complex of human Importin-9 with one homodimer of Akirin-2
Map dataPost processed map (using DeepEMhancer)
Sample
  • Complex: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
    • Protein or peptide: Akirin-2
    • Protein or peptide: Importin-9
Keywords20S proteasome / 20S / proteasome / nuclear import / akirin / akirin2 / importin 9 / importin / PROTEIN TRANSPORT
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 / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Akirin-2 / Importin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBrunner HL / Grundmann L / David H
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 26, 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_53266.png

Downloads & links

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Map

FileDownload / File: emd_53266.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost processed map (using DeepEMhancer)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.59 Å/pix.
x 120 pix.
= 190.2 Å		1.59 Å/pix.
x 120 pix.
= 190.2 Å		1.59 Å/pix.
x 120 pix.
= 190.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.585 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0495
Minimum - Maximum-0.010114188 - 1.799082
Average (Standard dev.)0.003028571 (±0.03903546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 190.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53266_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non postpricessed map

Fileemd_53266_additional_1.map
AnnotationNon postpricessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53266_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53266_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
    • Protein or peptide: Akirin-2
    • Protein or peptide: 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: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Akirin-2

MacromoleculeName: Akirin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.525582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MACGATLKRT LDFDPLLSPA SPKRRRCAPL SAPTSAAASP LSAAAATAAS FSAAAASPQK YLRMEPSPFG DVSSRLTTEQ ILYNIKQEY KRMQKRRHLE TSFQQTDPCC TSDAQPHAFL LSGPASPGTS SAASSPLKKE QPLFTLRQVG MICERLLKER E EKVREEYE ...String:
MACGATLKRT LDFDPLLSPA SPKRRRCAPL SAPTSAAASP LSAAAATAAS FSAAAASPQK YLRMEPSPFG DVSSRLTTEQ ILYNIKQEY KRMQKRRHLE TSFQQTDPCC TSDAQPHAFL LSGPASPGTS SAASSPLKKE QPLFTLRQVG MICERLLKER E EKVREEYE EILNTKLAEQ YDAFVKFTHD QIMRRYGEQP ASYVS

UniProtKB: Akirin-2

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Macromolecule #2: Importin-9

MacromoleculeName: Importin-9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 116.06232 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAAAAAGAA SGLPGPVAQG LKEALVDTLT GILSPVQEVR AAAEEQIKVL EVTEEFGVHL AELTVDPQGA LAIRQLASVI LKQYVETHW CAQSEKFRPP ETTERAKIVI RELLPNGLRE SISKVRSSVA YAVSAIAHWD WPEAWPQLFN LLMEMLVSGD L NAVHGAMR ...String:
MAAAAAAGAA SGLPGPVAQG LKEALVDTLT GILSPVQEVR AAAEEQIKVL EVTEEFGVHL AELTVDPQGA LAIRQLASVI LKQYVETHW CAQSEKFRPP ETTERAKIVI RELLPNGLRE SISKVRSSVA YAVSAIAHWD WPEAWPQLFN LLMEMLVSGD L NAVHGAMR VLTEFTREVT DTQMPLVAPV ILPEMYKIFT MAEVYGIRTR SRAVEIFTTC AHMICNMEEL EKGAAKVLIF PV VQQFTEA FVQALQIPDG PTSDSGFKME VLKAVTALVK NFPKHMVSSM QQILPIVWNT LTESAAFYVR TEVNYTEEVE DPV DSDGEV LGFENLVFSI FEFVHALLEN SKFKSTVKKA LPELIYYIIL YMQITEEQIK VWTANPQQFV EDEDDDTFSY TVRI AAQDL LLAVATDFQN ESAAALAAAA TRHLQEAEQT KNSGTEHWWK IHEACMLALG SVKAIITDSV KNGRIHFDMH GFLTN VILA DLNLSVSPFL LGRALWAASR FTVAMSPELI QQFLQATVSG LHETQPPSVR ISAVRAIWGY CDQLKVSEST HVLQPF LPS ILDGLIHLAA QFSSEVLNLV METLCIVCTV DPEFTASMES KICPFTIAIF LKYSNDPVVA SLAQDIFKEL SQIEACQ GP MQMRLIPTLV SIMQAPADKI PAGLCATAID ILTTVVRNTK PPLSQLLICQ AFPAVAQCTL HTDDNATMQN GGECLRAY V SVTLEQVAQW HDEQGHNGLW YVMQVVSQLL DPRTSEFTAA FVGRLVSTLI SKAGRELGEN LDQILRAILS KMQQAETLS VMQSLIMVFA HLVHTQLEPL LEFLCSLPGP TGKPALEFVM AEWTSRQHLF YGQYEGKVSS VALCKLLQHG INADDKRLQD IRVKGEEIY SMDEGIRTRS KSAKNPERWT NIPLLVKILK LIINELSNVM EANAARQATP AEWSQDDSND MWEDQEEEEE E EEDGLAGQ LLSDILATSK YEEDYYEDDE EDDPDALKDP LYQIDLQAYL TDFLCQFAQQ PCYIMFSGHL NDNERRVLQT IG I

UniProtKB: Importin-9

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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 R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 360044
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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