|Entry||Database: EMDB / ID: EMD-0621|
|Title||Structure of the AAV2 with its Cell Receptor, AAVR|
|Sample||AAV2 complex with AAVR receptor|
|Biological species||Adeno-associated virus|
|Method||subtomogram averaging / cryo EM / Resolution: 20 Å|
|Authors||Hu GQ / Meyer NL / Stagg SM / Chapman MS / Davulcu O / Xie Q / Noble AJ / Yoshioka C / Gingerich D / Trzynka A / David L|
|Citation||Journal: Elife / Year: 2019|
Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR.
Authors: Nancy L Meyer / Guiqing Hu / Omar Davulcu / Qing Xie / Alex J Noble / Craig Yoshioka / Drew S Gingerich / Andrew Trzynka / Larry David / Scott M Stagg / Michael Stewart Chapman /
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 ...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. -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. -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.
|Date||Deposition: Mar 1, 2019 / Header (metadata) release: Mar 27, 2019 / Map release: Jun 5, 2019 / Update: Jun 5, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0621.map.gz / Format: CCP4 / Size: 182.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 15.6 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire AAV2 complex with AAVR receptor
|Entire||Name: AAV2 complex with AAVR receptor / Details: class 1 / Number of components: 1|
-Component #1: protein, AAV2 complex with AAVR receptor
|Protein||Name: AAV2 complex with AAVR receptor / Details: class 1 / Recombinant expression: No|
|Mass||Theoretical: 3.75 MDa|
|Source||Species: Adeno-associated virus / Strain: hybrid of serotypes 2, 8, and 9|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm) / Vector: pFBDDJM11 / Strain: SF9 / Cell of expression system: Sf9|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.6 mg/mL|
Buffer solution: blot force = 1, blot time = 3 seconds, total blots = 1
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Details: preliminary grid screening was performed manually|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.42 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 18000.0 X (nominal), 18000.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 9000.0 - 11.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (290.0 - 300.0 K)|
|Camera||Detector: DIRECT ELECTRON DE-20 (5k x 3k)|
|Image acquisition||Sampling size: 10 µm / Details: none|
|Processing||Method: subtomogram averaging / Applied symmetry: I (icosahedral) / Number of subtomograms: 1321 / Number of class averages: 20 / Details: nond|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: Dynamo / CTF correction: tomoctf / Resolution: 20 Å / Resolution method: OTHER / Details: none / Euler angles: none|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Target criteria: correlation coeeficient / Refinement space: REAL|
Input PDB model: 6NZ0
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