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- EMDB-23634: AAV3 in liquid phase -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-23634
TitleAAV3 in liquid phase
Map data
Sample
  • Virus: Adeno-associated virus - 3
KeywordsAAV3 / AAV / cryoem / pdb / map / virus / liquid-phase
Biological speciesAdeno-associated virus - 3
Methodsingle particle reconstruction / Resolution: 5.0 Å
AuthorsJonaid GM / Kelly DF
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA193578, R01CA227261, R01CA219700 United States
CitationJournal: Adv Mater / Year: 2021
Title: High-Resolution Imaging of Human Viruses in Liquid Droplets.
Authors: G M Jonaid / William J Dearnaley / Michael A Casasanta / Liam Kaylor / Samantha Berry / Madeline J Dukes / Michael S Spilman / Jennifer L Gray / Deborah F Kelly /
Abstract: Liquid-phase electron microscopy (LP-EM) is an exciting new area in the materials imaging field, providing unprecedented views of molecular processes. Time-resolved insights from LP-EM studies are a ...Liquid-phase electron microscopy (LP-EM) is an exciting new area in the materials imaging field, providing unprecedented views of molecular processes. Time-resolved insights from LP-EM studies are a strong complement to the remarkable results achievable with other high-resolution techniques. Here, the opportunities to expand LP-EM technology beyond 2D temporal assessments and into the 3D regime are described. The results show new structures and dynamic insights of human viruses contained in minute volumes of liquid while acquired in a rapid timeframe. To develop this strategy, adeno-associated virus (AAV) is used as a model system. AAV is a well-known gene therapy vehicle with current applications involving drug delivery and vaccine development for COVID-19. Improving the understanding of the physical properties of biological entities in a liquid state, as maintained in the human body, has broad societal implications for human health and disease.
History
DepositionMar 17, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_23634.png

Downloads & links

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Map

FileDownload / File: emd_23634.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.00507
Minimum - Maximum-0.020897143 - 0.021350265
Average (Standard dev.)0.0006894457 (±0.0029842511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Adeno-associated virus - 3

EntireName: Adeno-associated virus - 3
Components
  • Virus: Adeno-associated virus - 3

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Supramolecule #1: Adeno-associated virus - 3

SupramoleculeName: Adeno-associated virus - 3 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 46350 / Sci species name: Adeno-associated virus - 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Diameter: 250.0 Å

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
GridMaterial: SILICON NITRIDE

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Electron microscopy

MicroscopeTFS TALOS F200C
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Detector mode: OTHER / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 1
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 16800

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Atomic model buiding 1

Initial modelPDB ID:

3kic


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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