9NZ1 | pdb_00009nz1

Adeno-associated virus serotype 11 basic regions in complex with importin alpha 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NZ1

This is version 1.0 of the entry. See complete history

Literature

Elucidation of the binding interaction interface between AAV serotype 11 capsid protein and host nuclear import proteins.

Hoad, M.Nematollahzadeh, S.Roby, J.A.Alvisi, G.Forwood, J.K.

(2025) Mol Ther Methods Clin Dev 33: 101630-101630

  • DOI: https://doi.org/10.1016/j.omtm.2025.101630
  • Primary Citation Related Structures: 
    9NZ1

  • PubMed Abstract: 

    Adeno-associated viruses (AAVs) are widely acknowledged as versatile vectors for gene therapy due to their non-pathogenic nature, inherent capacity for tissue-specific targeting, and their potential for customizable engineering. The N terminus of the AAV capsid protein VP1 plays a pivotal role in guiding AAV capsids into the cell nucleus. However, the precise dynamics of the interaction between the VP1 protein and host nuclear transport proteins, especially across diverse AAV serotypes, remain incompletely understood. AAV11 has emerged as a promising alternative for individuals with elevated antibody titers against AAV2, and in the field of neuroscience, it has demonstrated a strong capability for mapping and manipulating neural circuits, offering the potential for treating neurological and neurodegenerative disorders. In this study, we characterize the molecular interface between AAV11 VP1 and host importin-α (IMPα). Structural and biochemical analyses reveal that the basic regions BR1 and BR3 of the VP1 N-terminal domain engage IMPα in a bipartite nuclear localization signal (NLS)-like manner. These findings provide mechanistic insight into VP1-IMPα recognition and suggest a role for these interactions in AAV11 nuclear import. While direct functional evidence is pending, this work establishes the molecular basis for VP1-host protein binding and informs future capsid engineering.


  • Organizational Affiliation
    • School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.

Macromolecule Content 

  • Total Structure Weight: 61.81 kDa 
  • Atom Count: 3,389 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 570 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit alpha-1510Mus musculusMutation(s): 0 
Gene Names: Kpna2Rch1
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus)
Explore P52293 
Go to UniProtKB:  P52293
IMPC:  MGI:103561
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52293
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein60Adeno-associated virus 11Mutation(s): 0 
UniProt
Find proteins for Q5Y9B2 (Adeno-associated virus 11)
Explore Q5Y9B2 
Go to UniProtKB:  Q5Y9B2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Y9B2
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.525α = 90
b = 90.634β = 90
c = 98.992γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction

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: 2025-12-24
    Type: Initial release