6IH9 | pdb_00006ih9

Adeno-Associated Virus 2 at 2.8 ang

• PDB DOI: https://doi.org/10.2210/pdb6IH9/pdb
• EM Map EMD-9671: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Adeno-associated virus 2 Srivastava/1982
• Mutation(s): No 


• Deposited: 2018-09-29 Released: 2019-07-03 
• Deposition Author(s): Lou, Z.Y., Zhang, R.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 30742069 
• 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.

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Organizational Affiliation: 
• MOE Laboratory of Protein Science and Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China.
School of Life Sciences, Tsinghua University, Beijing, China.
State Key Laboratory of Medicinal Chemical Biology, College of Life Science and Pharmacy, Nankai University, Tianjin, China.
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.
Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK.
The Experimental High School Affiliated to Beijing Normal University, Beijing, China.
The High School Affiliated to Renmin University, Beijing, China.
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China. [e-mail].
MOE Laboratory of Protein Science and Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 58.64 kDa 
• Atom Count: 4,143 
• Modeled Residue Count: 517 
• Deposited Residue Count: 517 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	517	Adeno-associated virus 2 Srivastava/1982	Mutation(s): 0
UniProt
Find proteins for P03135 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore P03135  Go to UniProtKB:  P03135

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	2.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Lou, Z.Y., Zhang, R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21572116

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Other
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2025-07-02
  Changes: Data collection, Structure summary