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

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Basic information

Entry
Database: PDB / ID: 10sm
TitleImportin-9 bound to ETS homologous factor (EHF)
Components
  • ETS homologous factor
  • Importin-9
KeywordsNUCLEAR PROTEIN / Nuclear Import / Importin / DNA-binding protein / winged-helix domain
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBernardes, N.E. / Lankford, K. / McConville, M. / Chook, Y.M. / Liszczak, G.
Funding support United States, 6items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 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

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Assembly

Deposited unit
A: ETS homologous factor
D: Importin-9


Theoretical massNumber of molelcules
Total (without water)151,0002
Polymers151,0002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ETS homologous factor / hEHF / ETS domain-containing transcription factor / Epithelium-specific Ets transcription factor 3 / ESE-3


Mass: 34937.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHF, ESE3, ESE3B, ESEJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZC4
#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: Complex of Importin-9 with EHF / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.125 MDa / Experimental 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 type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 2200 nm / Nominal defocus min: 900 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6n1z

6n1z


Accession code: 6n1z / Source name: PDB / Type: experimental model

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