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- EMDB-29925: Cryo-tomogram of the Mega GVs -

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Basic information

Entry
Database: EMDB / ID: EMD-29925
TitleCryo-tomogram of the Mega GVs
Map dataTomogram of the Mega GVs
Sample
  • Organelle or cellular component: Gas vesicles
KeywordsGas vesicles / Flotation / cyanobacteria / CYTOSOLIC PROTEIN
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
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_29925.png

Downloads & links

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Map

FileDownload / File: emd_29925.map.gz / Format: CCP4 / Size: 386.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of the Mega GVs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8 Å/pix.
x 275 pix.
= 2200. Å		8 Å/pix.
x 720 pix.
= 5760. Å		8 Å/pix.
x 512 pix.
= 4096. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-53.676690000000001 - 53.681730000000002
Average (Standard dev.)0.55318356 (±2.9945617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin104-104138
Dimensions720512275
Spacing512720275
CellA: 4096.0 Å / B: 5760.0 Å / C: 2200.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Gas vesicles

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

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Supramolecule #1: Gas vesicles

SupramoleculeName: Gas vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Halobacterium salinarum NRC-1 (Halophile)

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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
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
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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