9QF0 | pdb_00009qf0

Cryo-EM structure of the mportin7:Histone H1.0 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Alphafold 3-guided insights into the Importin beta : Importin7 heterodimer interaction and its binding to histone H1.

Neumann, P.Dybkov, O.Urlaub, H.Ficner, R.Dickmanns, A.

(2026) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.12.011
  • Primary Citation of Related Structures:  
    9QEJ, 9QF0

  • PubMed Abstract: 

    The nuclear import of H1 linker histones is facilitated by a heterodimer of the transport receptors Importinβ (Impβ) and Importin7 (Imp7). The interaction between them is mediated by a stretch of C-terminal residues of Imp7 essential also for Imp7 activation by Impβ. An Impβ:Imp7:H1 complex model was predicted by Alphafold3 and validated using cross-linking data, isothermal titration calorimetry, and pull-down experiments, providing robust support for its accuracy. This model positions the H1 globular domain within the central cavity of Imp7. Refinement of this atomic model against a published cryo-electron microscopy (cryo-EM) map demonstrated significantly improved correspondence compared to the earlier interpretation, which placed the H1 globular domain within Impβ. This enhanced structural consistency further substantiates the accuracy of the AI-driven prediction. Moreover, a detailed analysis confirmed the extended C-terminal stretch of Imp7 harboring a nucleoporin-like binding (NlB) region with two FXFG-like nucleoporin motifs interacting with the outer surface of Impβ.


  • Organizational Affiliation
    • Department of Molecular Structural Biology, Institute for Microbiology and Genetics & GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. Electronic address: pneuman2@uni-goettingen.de.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Importin 7 L homeolog1,038Xenopus laevisMutation(s): 0 
Gene Names: ipo7.Limp7ipo7MGC52556ranbp7
UniProt
Find proteins for O42480 (Xenopus laevis)
Explore O42480 
Go to UniProtKB:  O42480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO42480
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H1.0B [auth C]194Homo sapiensMutation(s): 0 
Gene Names: H1-0H1F0H1FV
UniProt & NIH Common Fund Data Resources
Find proteins for P07305 (Homo sapiens)
Explore P07305 
Go to UniProtKB:  P07305
PHAROS:  P07305
GTEx:  ENSG00000189060 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07305
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
MODEL REFINEMENTRosettaEMrosetta.source.release-371

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references