7S1W

The AAVrh.10-glycan complex

  • Classification: VIRUS
  • Organism(s): Adeno-associated virus
  • Mutation(s): Yes 

  • Deposited: 2021-09-02 Released: 2021-09-22 
  • Deposition Author(s): Mietzsch, M., McKenna, R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Study of Aavrh.10 Receptor and Antibody Interactions.

Mietzsch, M.Yu, J.C.Hsi, J.Chipman, P.Broecker, F.Fuming, Z.Linhardt, R.J.Seeberger, P.H.Heilbronn, R.McKenna, R.Agbandje-McKenna, M.

(2021) J Virol 95: e0124921-e0124921

  • DOI: https://doi.org/10.1128/JVI.01249-21
  • Primary Citation of Related Structures:  
    7RL1, 7S1W

  • PubMed Abstract: 

    Recombinant adeno-associated virus (rAAV) vectors are one of the leading tools for the delivery of therapeutic genes in human gene therapy applications. For a successful transfer of their payload, the AAV vectors have to circumvent potential preexisting neutralizing host antibodies and bind to the receptors of the target cells. Both of these aspects have not been structurally analyzed for AAVrh.10. Here, cryo-electron microscopy and three-dimensional image reconstruction were used to map the binding site of sulfated N -acetyllactosamine (LacNAc; previously shown to bind AAVrh.10) and a series of four monoclonal antibodies (MAbs). LacNAc was found to bind to a pocket located on the side of the 3-fold capsid protrusion that is mostly conserved to AAV9 and equivalent to its galactose-binding site. As a result, AAVrh.10 was also shown to be able to bind to cell surface glycans with terminal galactose. For the antigenic characterization, it was observed that several anti-AAV8 MAbs cross-react with AAVrh.10. The binding sites of these antibodies were mapped to the 3-fold capsid protrusions. Based on these observations, the AAVrh.10 capsid surface was engineered to create variant capsids that escape these antibodies while maintaining infectivity. IMPORTANCE Gene therapy vectors based on adeno-associated virus rhesus isolate 10 (AAVrh.10) have been used in several clinical trials to treat monogenetic diseases. However, compared to other AAV serotypes little is known about receptor binding and antigenicity of the AAVrh.10 capsid. Particularly, preexisting neutralizing antibodies against capsids are an important challenge that can hamper treatment efficiency. This study addresses both topics and identifies critical regions of the AAVrh.10 capsid for receptor and antibody binding. The insights gained were utilized to generate AAVrh.10 variants capable of evading known neutralizing antibodies. The findings of this study could further aid the utilization of AAVrh.10 vectors in clinical trials and help the approval of the subsequent biologics.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Floridagrid.15276.37, Gainesville, Florida, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1520Adeno-associated virusMutation(s): 3 
UniProt
Find proteins for Q6JC62 (Adeno-associated virus)
Explore Q6JC62 
Go to UniProtKB:  Q6JC62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6JC62
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAL (Subject of Investigation/LOI)
Query on GAL

Download Ideal Coordinates CCD File 
AC [auth S]
AD [auth s]
BC [auth T]
BD [auth t]
CC [auth U]
AC [auth S],
AD [auth s],
BC [auth T],
BD [auth t],
CC [auth U],
CD [auth u],
DC [auth V],
DD [auth v],
EC [auth W],
ED [auth w],
FC [auth X],
FD [auth x],
GC [auth Y],
GD [auth y],
HC [auth Z],
HD [auth z],
IB [auth A],
IC [auth a],
ID [auth 1],
JB [auth B],
JC [auth b],
JD [auth 2],
KB [auth C],
KC [auth c],
KD [auth 3],
LB [auth D],
LC [auth d],
LD [auth 4],
MB [auth E],
MC [auth e],
MD [auth 5],
NB [auth F],
NC [auth f],
ND [auth 6],
OB [auth G],
OC [auth g],
OD [auth 7],
PB [auth H],
PC [auth h],
PD [auth 8],
QB [auth I],
QC [auth i],
RB [auth J],
RC [auth j],
SB [auth K],
SC [auth k],
TB [auth L],
TC [auth l],
UB [auth M],
UC [auth m],
VB [auth N],
VC [auth n],
WB [auth O],
WC [auth o],
XB [auth P],
XC [auth p],
YB [auth Q],
YC [auth q],
ZB [auth R],
ZC [auth r]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2021-11-24
    Changes: Database references
  • Version 1.3: 2021-12-01
    Changes: Database references