6V1G

Genome-containing AAVrh.10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 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

Comparative Analysis of the Capsid Structures of AAVrh.10, AAVrh.39, and AAV8.

Mietzsch, M.Barnes, C.Hull, J.A.Chipman, P.Xie, J.Bhattacharya, N.Sousa, D.McKenna, R.Gao, G.Agbandje-McKenna, M.

(2019) J.Virol. --: --

  • DOI: 10.1128/JVI.01769-19
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adeno-associated viruses (AAVs) from clade E are often used as vectors in gene delivery applications. This clade includes rhesus isolate 10 (AAVrh.10) and 39 (AAVrh.39) which, unlike representative AAV8, are capable of crossing the blood-brain barrie ...

    Adeno-associated viruses (AAVs) from clade E are often used as vectors in gene delivery applications. This clade includes rhesus isolate 10 (AAVrh.10) and 39 (AAVrh.39) which, unlike representative AAV8, are capable of crossing the blood-brain barrier (BBB) thereby enabling the delivery of therapeutic genes to the CNS. Here the capsid structures of AAV8, AAVrh.10 and AAVrh.39 have been determined by cryo-electron microscopy and three-dimensional image reconstruction to 3.08, 2.75, and 3.39 Å resolution, respectively, to enable a direct structural comparison. AAVrh.10 and AAVrh.39 are 98% identical in amino acid sequence but only ∼93.5% to AAV8. However, the capsid structures of all three viruses are similar with only minor differences observed in the previously described surface variable regions suggesting that the specific residues S269 and N472, absent in AAV8, may confer the ability to cross the BBB in AAVrh.10 and AAVrh.39. Head-to-head comparison of empty and genome-containing particles showed DNA ordered in the previously described nucleotide-binding pocket supporting the suggested role of this pocket in DNA packaging for the Dependoparvovirus The structural characterization of these viruses provides a platform for future vector engineering efforts towards improved gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity or receptor retargeting. Importance Recombinant adeno-associated virus vectors (rAAVs), based on AAV8 and AAVrh.10, have been utilized in multiple clinical trials to treat different monogenetic diseases. Closely related AAVrh.39 has also shown promise in vivo As recently attained for other AAV biologics, e.g. Luxturna and Zolgensma, based on AAV2 and AAV9, respectively, the vectors in this study will likely gain FDA approval for commercialization in the near future. The study characterized the capsid structures of these clinical vectors, at atomic resolution using cryo-EM and image reconstruction, for comparative analysis. The analysis suggested two key residues, S269 and N472, as determinants of BBB crossing for AAVrh.10 and AAVrh.39, a feature utilized for CNS delivery of therapeutic genes. The structure information thus provides a platform for engineering to improve receptor retargeting or tissue specificity. These are important challenges in the field that need attention. Capsid structure information also provides knowledge potentially applicable for regulatory product approval.


    Organizational Affiliation

    Horae Gene Therapy Center, Department of Microbiology and Physiological Systems, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA mckenna@ufl.edu.,Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA.,Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, 1, 2, 3, 4, 5, 6, 7, 8
520Adeno-associated virusMutation(s): 0 
Gene Names: cap
Find proteins for Q6JC62 (Adeno-associated virus)
Go to UniProtKB:  Q6JC62
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DC
Query on DC

Download SDF File 
Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, A, a, B, b, c, C, D, d, e, E, f, F, G, g, h, H, I, i, J, j, k, K, l, L, M, m, n, N, O, o, p, P, q, Q, R, r, s, S, t, T, u, U, v, V, W, w, x, X, Y, y, z, Z
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
 Ligand Interaction
DA
Query on DA

Download SDF File 
Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, A, a, b, B, c, C, D, d, e, E, f, F, g, G, H, h, i, I, J, j, k, K, L, l, M, m, N, n, o, O, P, p, q, Q, R, r, s, S, T, t, U, u, V, v, w, W, x, X, y, Y, Z, z
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references