9B7K | pdb_00009b7k

Fab2-1 in complex with the capsid of Adeno-associated virus type 9


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of antibody-responses following Zolgensma treatment for AAV capsid engineering to expand patient cohorts.

Mietzsch, M.Hsi, J.Nelson, A.R.Khandekar, N.Huang, A.M.Smith, N.J.Zachary, J.Potts, L.Farrar, M.A.Chipman, P.Ghanem, M.Alexander, I.E.Logan, G.J.Huiskonen, J.T.McKenna, R.

(2025) Nat Commun 16: 3731-3731

  • DOI: https://doi.org/10.1038/s41467-025-59088-4
  • Primary Citation of Related Structures:  
    9B6N, 9B6O, 9B6P, 9B6Q, 9B6R, 9B6S, 9B6T, 9B7K, 9B7L, 9B7M, 9B7N, 9B7O, 9B7P, 9B7Q, 9B7R, 9B7S, 9B7T, 9B7U, 9B7V, 9B7W, 9B7X

  • PubMed Abstract: 

    Monoclonal antibodies are useful tools to dissect the neutralizing antibody response against the adeno-associated virus (AAV) capsids that are used as gene therapy delivery vectors. The presence of pre-existing neutralizing antibodies in large portions of the human population poses a significant challenge for AAV-mediated gene therapy, primarily targeting the capsid leading to vector inactivation and loss of treatment efficacy. This study structurally characterizes the interactions of 21 human-derived neutralizing antibodies from three patients treated with the AAV9 vector, Zolgensma®, utilizing high-resolution cryo-electron microscopy. The antibodies bound to the 2-fold depression or the 3-fold protrusions do not conform to the icosahedral symmetry of the capsid, thus requiring localized reconstructions. These complex structures provide unprecedented details of the mAbs binding interfaces, with many antibodies inducing structural perturbations of the capsid upon binding. Key surface capsid amino acid residues were identified facilitating the design of capsid variants with antibody escape phenotypes. These AAV9 capsid variants have the potential to expand the patient cohort to include those that were previously excluded due to their pre-existing neutralizing antibodies against the wtAAV9 capsid, and the possibly of further treatment to those requiring redosing.


  • Organizational Affiliation
    • Department of Biochemistry & Molecular Biology, Center for Structural Biology, McKnight Brain Institute. College of Medicine, University of Florida, Gainesville, FL, USA. mario.mietzsch@ufl.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1
A, B, C, D, E
A, B, C, D, E, F
534Adeno-associated virusMutation(s): 0 
Gene Names: cap
UniProt
Find proteins for Q6JC40 (Adeno-associated virus 9)
Explore Q6JC40 
Go to UniProtKB:  Q6JC40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6JC40
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab2-1 heavy chainG [auth H]131Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab2-1 light chainH [auth L]110Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM082946

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection
  • Version 1.2: 2025-06-11
    Changes: Data collection, Database references