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- EMDB-29922: Cryo-tomogram of the native Ana GV -

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Basic information

Entry
Database: EMDB / ID: EMD-29922
TitleCryo-tomogram of the native Ana GV
Map dataTomogram of the native Ana GV
Sample
  • Organelle or cellular component: Native Gas vesicles
KeywordsGas vesicles / Flotation / cyanobacteria / CYTOSOLIC PROTEIN
Biological speciesDolichospermum flos-aquae (bacteria)
Methodelectron tomography / cryo EM
AuthorsDutka P / Metskas LA / Hurt RC / Salahshoor H / Wang TY / Malounda D / Lu GJ / Chou TF / Shapiro MG / Jensen JJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127401 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)EB018975 United States
CitationJournal: Structure / Year: 2023
Title: Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET.
Authors: Przemysław Dutka / Lauren Ann Metskas / Robert C Hurt / Hossein Salahshoor / Ting-Yu Wang / Dina Malounda / George J Lu / Tsui-Fen Chou / Mikhail G Shapiro / Grant J Jensen /
Abstract: Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical ...Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.
History
DepositionFeb 28, 2023-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29922.png

Downloads & links

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Map

FileDownload / File: emd_29922.map.gz / Format: CCP4 / Size: 386.3 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of the native Ana GV
Voxel sizeX=Y=Z: 6.748 Å
Density
Minimum - Maximum-128.0 - 119.0
Average (Standard dev.)0.0755149 (±17.324141999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-138209-209
Dimensions14401023275
Spacing10231440275
CellA: 6903.204 Å / B: 9717.12 Å / C: 1855.7001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Native Gas vesicles

EntireName: Native Gas vesicles
Components
  • Organelle or cellular component: Native Gas vesicles

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Supramolecule #1: Native Gas vesicles

SupramoleculeName: Native Gas vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Dolichospermum flos-aquae (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5 / Details: 10 mM HEPES, pH 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: eTomo / Software - details: SIRT-like / Number images used: 41

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