Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 120-mer - A60B60 

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

Macromolecule Content

• Total Structure Weight: 113.94 kDa 
• Atom Count: 4884 
• Modelled Residue Count: 594 
• Deposited Residue Count: 1025 
• Unique protein chains: 2

6NZ0

Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2

• DOI: 10.2210/pdb6NZ0/pdb
• EMDataResource: EMD-0553

• Classification: VIRUS
• Organism(s): Homo sapiens, Adeno-associated virus 2 Srivastava/1982
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-02-12 Released: 2019-06-12 
• Deposition Author(s): Meyer, N.L., Xie, Q., Davulcu, O., Yoshioka, C., Chapman, M.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR.

Meyer, N.L., Hu, G., Davulcu, O., Xie, Q., Noble, A.J., Yoshioka, C., Gingerich, D.S., Trzynka, A., David, L., Stagg, S.M., Chapman, M.S.

(2019) Elife 8

• PubMed: 31115336 
• DOI: 10.7554/eLife.44707
• Primary Citation of Related Structures:  
  6NZ0


• PubMed Abstract: 
  

Adeno-associated virus (AAV) vectors are preeminent in emerging clinical gene therapies. Generalizing beyond the most tractable genetic diseases will require modulation of cell specificity and immune neutralization. Interactions of AAV with its cellular receptor, AAVR, are key to understanding cell-entry and trafficking with the rigor needed to engineer tissue-specific vectors. Cryo -electron tomography shows ordered binding of part of the flexible receptor to the viral surface, with distal domains in multiple conformations. Regions of the virus and receptor in close physical proximity can be identified by cross-linking/mass spectrometry. Cryo -electron microscopy with a two-domain receptor fragment reveals the interactions at 2.4 Å resolution. AAVR binds between AAV's spikes on a plateau that is conserved, except in one clade whose structure is AAVR-incompatible. AAVR's footprint overlaps the epitopes of several neutralizing antibodies, prompting a re-evaluation of neutralization mechanisms. The structure provides a roadmap for experimental probing and manipulation of viral-receptor interactions.

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Organizational Affiliation: 

Department of Biochemistry, University of Missouri, Columbia, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dyslexia-associated protein KIAA0319-like protein	Z	290	Homo sapiens	Mutation(s): 0  Gene Names: KIAA0319L, AAVR, KIAA1837, PP791
Find proteins for Q8IZA0 (Homo sapiens) Explore Q8IZA0  Go to UniProtKB:  Q8IZA0
NIH Common Fund Data Resources
PHAROS:  Q8IZA0 GTEx:  ENSG00000142687

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	735	Adeno-associated virus 2 Srivastava/1982	Mutation(s): 0  Gene Names: VP1
Find proteins for P03135 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore P03135  Go to UniProtKB:  P03135

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	Z	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-02-12 
• Released Date: 2019-06-12 
Deposition Author(s): Meyer, N.L., Xie, Q., Davulcu, O., Yoshioka, C., Chapman, M.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM122564
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM066875

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-06-19
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence, Other