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- EMDB-0622: Structure of the AAV2 with its Cell Receptor, AAVR -

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Basic information

Entry
Database: EMDB / ID: EMD-0622
TitleStructure of the AAV2 with its Cell Receptor, AAVR
Map dataAAV2 bound with AAVR (class2)
Sample
  • Complex: AAV2 complex with AAVR receptor
Biological speciesAdeno-associated virus
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 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.
History
DepositionMar 1, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseJun 5, 2019-
UpdateJun 5, 2019-
Current statusJun 5, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0622.png

Downloads & links

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Map

FileDownload / File: emd_0622.map.gz / Format: CCP4 / Size: 182.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAAV2 bound with AAVR (class2)
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 15.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.4832658 - 2.3566298
Average (Standard dev.)0.0018600414 (±0.2926803)
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-1.4832.3570.002

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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
Components
  • Complex: AAV2 complex with AAVR receptor

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Supramolecule #1: AAV2 complex with AAVR receptor

SupramoleculeName: AAV2 complex with AAVR receptor / type: complex / ID: 1 / Parent: 0 / Details: class 1
Source (natural)Organism: Adeno-associated virus / Strain: hybrid of serotypes 2, 8, and 9
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: SF9 / Recombinant cell: Sf9 / Recombinant plasmid: pFBDDJM11
Molecular weightTheoretical: 3.75 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
25.0 mMMgCl2magnesium chloride
25.0 mMNaClsodium chloride

Details: blot force = 1, blot time = 3 seconds, total blots = 1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 290.0 K / Max: 300.0 K
Detailspreliminary grid screening was performed manually
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5000 pixel / Digitization - Dimensions - Height: 3000 pixel / Digitization - Sampling interval: 10.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Average exposure time: 1.5 sec. / Average electron dose: 1.42 e/Å2 / Details: none
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 0.011 µm / Calibrated defocus min: 9.0 µm / Calibrated magnification: 18000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.011 µm / Nominal defocus min: 9.0 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsnond
Final reconstructionNumber classes used: 20 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: Dynamo (ver. 1.0) / Software - details: none / Details: none / Number subtomograms used: 8
ExtractionNumber tomograms: 8 / Number images used: 1321 / Reference model: AAVDJ low passfilter to 50 agntrom / Method: automatic / Software - Name: Dynamo (ver. 1) / Details: none
CTF correctionSoftware - Name: TOMOCTF (ver. 1.0) / Software - details: none / Details: tomoctf
Final 3D classificationNumber classes: 20 / Avg.num./class: 150 / Details: none
Final angle assignmentType: COMMON LINE / Software - Name: Dynamo (ver. 1) / Software - details: none / Details: none

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Atomic model buiding 1

Initial modelPDB ID:

6nz0

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coeeficient

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