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- EMDB-0624: Structure of the AAV2 with its Cell Receptor, AAVR -

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Basic information

Entry
Database: EMDB / ID: EMD-0624
TitleStructure of the AAV2 with its Cell Receptor, AAVR
Map data
SampleAAV2 complex with AAVR receptor
Biological speciesAdeno-associated virus
Methodelectron tomography / cryo EM / Resolution: 10 Å
AuthorsHu GQ / Meyer NL / Stagg SM / Chapman MS / Davulcu O / Xie Q / Noble AJ / Yoshioka C / Gingerich D / Trzynka A / David L
CitationJournal: 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.
DateDeposition: Mar 1, 2019 / Header (metadata) release: Jun 5, 2019 / Map release: Jun 5, 2019 / Update: Jun 5, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_0624.map.gz / Format: CCP4 / Size: 182.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.6 Å/pix.
x 36 pix.
= 561.6 Å
15.6 Å/pix.
x 36 pix.
= 561.6 Å
15.6 Å/pix.
x 36 pix.
= 561.6 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 15.6 Å
Density
Contour LevelMovie #1: 0.22
Minimum - Maximum-1.4722327 - 2.4081862
Average (Standard dev.)0.0019994653 (±0.3053637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-18-18-18
Dimensions363636
Spacing363636
CellA=B=C: 561.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z15.615.615.6
M x/y/z363636
origin x/y/z0.0000.0000.000
length x/y/z561.600561.600561.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-18-18-18
NC/NR/NS363636
D min/max/mean-1.4722.4080.002

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Supplemental data

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Sample components

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Entire AAV2 complex with AAVR receptor

EntireName: AAV2 complex with AAVR receptor / Details: class 1 / Number of components: 1

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Component #1: protein, AAV2 complex with AAVR receptor

ProteinName: AAV2 complex with AAVR receptor / Details: class 1 / Recombinant expression: No
MassTheoretical: 3.75 MDa
SourceSpecies: 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

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.6 mg/mL
Buffer solution: blot force = 1, blot time = 3 seconds, total blots = 1
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: preliminary grid screening was performed manually
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.42 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000.0 X (nominal), 18000.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 9000.0 - 11.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (290.0 - 300.0 K)
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image acquisition

Image acquisitionSampling size: 10 µm / Details: none

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Image processing

ProcessingMethod: electron tomography / Number of sections: 280 / Details: nond
3D reconstructionAlgorithm: BACK PROJECTION / Software: Dynamo / CTF correction: tomoctf / Resolution: 10 Å / Resolution method: OTHER / Details: none

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: correlation coeeficient / Refinement space: REAL
Input PDB model: 6NZ0

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