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 6IHB | pdb_00006ihb

Adeno-Associated Virus 2 in complex with AAVR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6IHB

This is version 1.4 of the entry. See complete history. 

Literature

Adeno-associated virus 2 bound to its cellular receptor AAVR.

Zhang, R., Cao, L., Cui, M., Sun, Z., Hu, M., Zhang, R., Stuart, W., Zhao, X., Yang, Z., Li, X., Sun, Y., Li, S., Ding, W., Lou, Z., Rao, Z.

(2019) Nat Microbiol 4: 675-682

  • DOI: https://doi.org/10.1038/s41564-018-0356-7
  • Primary Citation Related Structures: 
    6IH9, 6IHB

  • PubMed Abstract: 

    Adeno-associated virus (AAV) is a leading vector for virus-based gene therapy. The receptor for AAV (AAVR; also named KIAA0319L) was recently identified, and the precise characterization of AAV-AAVR recognition is in immediate demand. Taking advantage of a particle-filtering algorithm, we report here the cryo-electron microscopy structure of the AAV2-AAVR complex at 2.8 Å resolution. This structure reveals that of the five Ig-like polycystic kidney disease (PKD) domains in AAVR, PKD2 binds directly to the spike region of the AAV2 capsid adjacent to the icosahedral three-fold axis. Residues in strands B and E, and the BC loop of AAVR PKD2 interact directly with the AAV2 capsid. The interacting residues in the AAV2 capsid are mainly in AAV-featured variable regions. Mutagenesis of the amino acids at the AAV2-AAVR interface reduces binding activity and viral infectivity. Our findings provide insights into the biology of AAV entry with high-resolution details, providing opportunities for the development of new AAV vectors for gene therapy.


  • Organizational Affiliation: 
    • MOE Laboratory of Protein Science and Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 92.35 kDa 
  • Atom Count: 4,868 
  • Modeled Residue Count: 611 
  • Deposited Residue Count: 829 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dyslexia-associated protein KIAA0319-like proteinA [auth R]94Homo sapiensMutation(s): 0 
Gene Names: KIAA0319L, AAVR, KIAA1837, PP791
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZA0 (Homo sapiens)
Explore Q8IZA0 
Go to UniProtKB:  Q8IZA0
PHAROS:  Q8IZA0
GTEx:  ENSG00000142687 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IZA0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein VP1B [auth A]735Adeno-associated virus 2 Srivastava/1982Mutation(s): 0 
UniProt
Find proteins for P03135 (Adeno-associated virus 2 (isolate Srivastava/1982))
Explore P03135 
Go to UniProtKB:  P03135
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03135
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: 2D ARRAY 
  • 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 Natural Science Foundation of ChinaChina21572116

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2025-06-25
    Changes: Data collection, Structure summary