7MTP

Structure of the adeno-associated virus 9 capsid at pH 5.5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 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

AAV9 Structural Rearrangements Induced by Endosomal Trafficking pH and Glycan Attachment.

Penzes, J.J.Chipman, P.Bhattacharya, N.Zeher, A.Huang, R.McKenna, R.Agbandje-McKenna, M.

(2021) J Virol : JVI0084321-JVI0084321

  • DOI: 10.1128/JVI.00843-21
  • Primary Citation of Related Structures:  
    7MT0, 7MTW, 7MTZ, 7MTP, 7MTG, 7MUA

  • PubMed Abstract: 
  • Adeno-associated viruses (AAVs) are small non-enveloped ssDNA viruses, that are currently being developed as gene therapy biologics. After cell entry, AAVs traffic to the nucleus using the endo-lysosomal pathway. The subsequent decrease in pH triggers conformational changes to the capsid that enables the externalization of the capsid protein (VP) N-termini, including the unique domain of the minor capsid protein VP1 (VP1u), which permits phospholipase activity required for the capsid lysosomal egress ...

    Adeno-associated viruses (AAVs) are small non-enveloped ssDNA viruses, that are currently being developed as gene therapy biologics. After cell entry, AAVs traffic to the nucleus using the endo-lysosomal pathway. The subsequent decrease in pH triggers conformational changes to the capsid that enables the externalization of the capsid protein (VP) N-termini, including the unique domain of the minor capsid protein VP1 (VP1u), which permits phospholipase activity required for the capsid lysosomal egress. Here, we report the AAV9 capsid structure, determined at the endosomal pHs (7.4, 6.0, 5.5, and 4.0) and terminal galactose-bound AAV9 capsids at pHs 7.4 and 5.5 using cryo-electron microscopy and three-dimensional image reconstruction. Taken together these studies provide insight into AAV9 capsid conformational changes at the 5-fold pore during endosomal trafficking, both in the presence and absence of its cellular glycan receptor. We visualized, for the first time, that acidification induces the externalization of the VP3 and possibly VP2 N-termini, presumably in prelude to the externalization of VP1u at pH 4.0, that is essential for lysosomal membrane disruption. In addition, the structural study of AAV9-galactose interactions demonstrates AAV9 remains attached to its glycan receptor at the late endosome pH 5.5. This interaction significantly alters the conformational stability of the variable region I of the VPs, as well as the dynamics associated with VP N-terminus externalization. Importance There are 13 distinct Adeno-associated virus (AAV) serotypes that are structurally homologous and whose capsid proteins (VP1-3) are similar in amino acid sequence. However, AAV9 is one of the most commonly studied and used as gene therapy vector. This is part because, AAV9 is capable of crossing the blood brain barrier as well as readily transduces a wide array of tissues, including the central nervous system. In this study we provide AAV9 capsid structural insight during intracellular trafficking. Although the AAV capsid has been shown to externalize the N-termini of its VPs, to enzymatically disrupt the lysosome membrane at low pH, there was no structural evidence to confirm this. By utilizing AAV9 as our model, we provide the first structural evidence that the externalization process occurs at the protein interface at the icosahedral 5-fold symmetry axis and can be triggered by lowering pH.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1518Adeno-associated virus 9Mutation(s): 0 
Gene Names: cap
UniProt
Find proteins for Q6JC40 (Adeno-associated virus 9)
Explore Q6JC40 
Go to UniProtKB:  Q6JC40
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR01 GM109524
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM082946
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10 OD018142
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10 RR025080
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM116788

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references