10SM | pdb_000010sm

Importin-9 bound to ETS homologous factor (EHF)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Importin-9 recognizes the winged-helix fold of ETS transcription factors to mediate nuclear import.

McConville, M.Lankford, K.Bernardes, N.E.Walterscheid, A.Valadez, C.Niesman, A.Chook, Y.M.Liszczak, G.

(2026) Proc Natl Acad Sci U S A 123: e2536763123-e2536763123

  • DOI: https://doi.org/10.1073/pnas.2536763123
  • Primary Citation Related Structures: 
    10SM

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390.

Macromolecule Content 

  • Total Structure Weight: 151 kDa 
  • Atom Count: 8,084 
  • Modeled Residue Count: 1,022 
  • Deposited Residue Count: 1,341 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ETS homologous factor300Homo sapiensMutation(s): 0 
Gene Names: EHFESE3ESE3BESEJ
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZC4 (Homo sapiens)
Explore Q9NZC4 
Go to UniProtKB:  Q9NZC4
PHAROS:  Q9NZC4
GTEx:  ENSG00000135373 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZC4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin-9B [auth D]1,041Homo sapiensMutation(s): 0 
Gene Names: IPO9IMP9KIAA1192RANBP9HSPC273
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P70 (Homo sapiens)
Explore Q96P70 
Go to UniProtKB:  Q96P70
PHAROS:  Q96P70
GTEx:  ENSG00000198700 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96P70
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR180051
Welch FoundationUnited StatesI-203920230405
Welch FoundationUnited StatesI-1532
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States5F30 HL167629
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35 GM147140
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM144137

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release