AAV5 in neutral condition at 3.18 Ang

  • Classification: VIRUS
  • Organism(s): adeno-associated virus 5
  • Mutation(s): No 

  • Deposited: 2019-01-30 Released: 2019-07-31 
  • Deposition Author(s): Lou, Z., Zhang, R.
  • Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

  • Resolution: 3.18 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Divergent engagements between adeno-associated viruses with their cellular receptor AAVR.

Zhang, R.Xu, G.Cao, L.Sun, Z.He, Y.Cui, M.Sun, Y.Li, S.Li, H.Qin, L.Hu, M.Yuan, Z.Rao, Z.Ding, W.Rao, Z.Lou, Z.

(2019) Nat Commun 10: 3760-3760

  • DOI: https://doi.org/10.1038/s41467-019-11668-x
  • Primary Citation of Related Structures:  
    6JCQ, 6JCR, 6JCS, 6JCT

  • PubMed Abstract: 

    Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, revealing the molecular details by which PKD1 recognizes AAV5 and PKD2 is solely engaged with AAV1. PKD2 lies on the plateau region of the AAV1 capsid. However, the AAV5-AAVR interface is strikingly different, in which PKD1 is bound at the opposite side of the spike of the AAV5 capsid than the PKD2-interacting region of AAV1. Residues in strands F/G and the CD loop of PKD1 interact directly with AAV5, whereas residues in strands B/C/E and the BC loop of PKD2 make contact with AAV1. These findings further the understanding of the distinct mechanisms by which AAVR recognizes various AAV serotypes and provide an example of a single receptor engaging multiple viral serotypes with divergent rules.

  • Organizational Affiliation

    High School Attached to Capital Normal University, Beijing, 100048, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein516adeno-associated virus 5Mutation(s): 0 
Gene Names: capVP1
Find proteins for Q9YIJ1 (adeno-associated virus 5)
Explore Q9YIJ1 
Go to UniProtKB:  Q9YIJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YIJ1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.18 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references