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- EMDB-75437: Importin-9 bound to ETS homologous factor (EHF) -

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Basic information

Entry
Database: EMDB / ID: EMD-75437
TitleImportin-9 bound to ETS homologous factor (EHF)
Map data
Sample
  • Complex: Complex of Importin-9 with EHF
    • Protein or peptide: ETS homologous factor
    • Protein or peptide: Importin-9
KeywordsNuclear Import / Importin / DNA-binding protein / winged-helix domain / NUCLEAR PROTEIN
Function / homology
Function and homology information


proteasome localization / histone chaperone activity / nuclear import signal receptor activity / epithelial cell differentiation / small GTPase binding / protein import into nucleus / nuclear envelope / DNA-binding transcription activator activity, RNA polymerase II-specific / histone binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...proteasome localization / histone chaperone activity / nuclear import signal receptor activity / epithelial cell differentiation / small GTPase binding / protein import into nucleus / nuclear envelope / DNA-binding transcription activator activity, RNA polymerase II-specific / histone binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
ETS homologous factor / : / Importin-11-like, TPR repeats / : / Importin-9 central HEAT repeats / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets domain ...ETS homologous factor / : / Importin-11-like, TPR repeats / : / Importin-9 central HEAT repeats / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Sterile alpha motif/pointed domain superfamily / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Importin-9 / ETS homologous factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBernardes NE / Lankford K / McConville M / Chook YM / Liszczak G
Funding support United States, 6 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR180051 United States
Welch FoundationI-203920230405 United States
Welch FoundationI-1532 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5F30 HL167629 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35 GM147140 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM144137 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Importin-9 recognizes the winged-helix fold of ETS transcription factors to mediate nuclear import.
Authors: Michael McConville / Kaylee Lankford / Natalia E Bernardes / Abby Walterscheid / Catherine Valadez / Ashley Niesman / Yuh Min Chook / Glen Liszczak /
Abstract: Protein trafficking between the cytoplasm and the nucleus is a fundamental process in eukaryotic cell biology. While linear nuclear localization signals (NLSs) are well characterized, many nuclear ...Protein trafficking between the cytoplasm and the nucleus is a fundamental process in eukaryotic cell biology. While linear nuclear localization signals (NLSs) are well characterized, many nuclear proteins lack a predictable NLS. Here, we identify the ETS domain, a DNA-binding winged-helix fold, from ETS family transcription factors as a structure-encoded NLS. We show that ETS domains mediate nuclear import through direct nanomolar affinity recognition by IPO9. Cryo-electron microscopy analysis of the EHF:IPO9 complex reveals that the IPO9 wraps around the ETS domain and engages structural features throughout the winged-helix fold. Biochemical studies demonstrate that the ETS domain DNA-binding helix is critical for importin recognition and for NLS activity in mammalian cells. Comparison of IPO9 bound to EHF and the histone H2A:H2B dimer reveals distinct interaction hotspots, illustrating how IPO9 employs unique combinatorial binding surfaces to accommodate structurally diverse cargos. These findings define a unique class of globular NLSs and highlight the adaptability of importins in recognizing distinct protein folds.
History
DepositionFeb 5, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75437.png

Downloads & links

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Map

FileDownload / File: emd_75437.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 240 pix.
= 298.8 Å		1.25 Å/pix.
x 240 pix.
= 298.8 Å		1.25 Å/pix.
x 240 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.0017784394 - 1.9643394
Average (Standard dev.)0.00068041653 (±0.019327259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75437_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_75437_half_map_2.map
Projections & Slices
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Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Importin-9 with EHF

EntireName: Complex of Importin-9 with EHF
Components
  • Complex: Complex of Importin-9 with EHF
    • Protein or peptide: ETS homologous factor
    • Protein or peptide: Importin-9

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Supramolecule #1: Complex of Importin-9 with EHF

SupramoleculeName: Complex of Importin-9 with EHF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125 KDa

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Macromolecule #1: ETS homologous factor

MacromoleculeName: ETS homologous factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.937223 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MILEGGGVMN LNPGNNLLHQ PPAWTDSYST CNVSSGFFGG QWHEIHPQYW TKYQVWEWLQ HLLDTNQLDA NCIPFQEFDI NGEHLCSMS LQEFTRAAGT AGQLLYSNLQ HLKWNGQCSS DLFQSTHNVI VKTEQTEPSI MNTWKDENYL YDTNYGSTVD L LDSKTFCR ...String:
MILEGGGVMN LNPGNNLLHQ PPAWTDSYST CNVSSGFFGG QWHEIHPQYW TKYQVWEWLQ HLLDTNQLDA NCIPFQEFDI NGEHLCSMS LQEFTRAAGT AGQLLYSNLQ HLKWNGQCSS DLFQSTHNVI VKTEQTEPSI MNTWKDENYL YDTNYGSTVD L LDSKTFCR AQISMTTTSH LPVAESPDMK KEQDPPAKCH TKKHNPRGTH LWEFIRDILL NPDKNPGLIK WEDRSEGVFR FL KSEAVAQ LWGKKKNNSS MTYEKLSRAM RYYYKREILE RVDGRRLVYK FGKNARGWRE NEN

UniProtKB: ETS homologous factor

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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 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: PDB ENTRY
PDB model - PDB ID:

6n1z

Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 120000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6n1z


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-10sm:
Importin-9 bound to ETS homologous factor (EHF)

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