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- EMDB-29921: Subtomogram average of the native Ana GV shell -

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Basic information

Entry
Database: EMDB / ID: EMD-29921
TitleSubtomogram average of the native Ana GV shell
Map datanative AnaGV map
Sample
  • Organelle or cellular component: Stripped Gas vesicles
Function / homology
Function and homology information


gas vesicle shell / vesicle membrane / structural molecule activity
Similarity search - Function
Gas vesicle protein GvpA / Gas vesicle protein GvpA, conserved site / : / : / Gas vesicle protein / Gas vesicles protein GVPa signature 1. / Gas vesicles protein GVPa signature 2.
Similarity search - Domain/homology
Gas vesicle protein A
Similarity search - Component
Biological speciesDolichospermum flos-aquae (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.0 Å
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 19, 2023-
Map releaseApr 19, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29921.png

Downloads & links

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Map

FileDownload / File: emd_29921.map.gz / Format: CCP4 / Size: 21.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnative AnaGV map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 178 pix.
= 300.286 Å		1.69 Å/pix.
x 178 pix.
= 300.286 Å		1.69 Å/pix.
x 178 pix.
= 300.286 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.687 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.638
Minimum - Maximum-0.7958028 - 1.40953
Average (Standard dev.)0.019408965 (±0.11571935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions178178178
Spacing178178178
CellA=B=C: 300.286 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29921_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: native AnaGV halfmap1

Fileemd_29921_half_map_1.map
Annotationnative AnaGV halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: native AnaGV halfmap2

Fileemd_29921_half_map_2.map
Annotationnative AnaGV halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Stripped Gas vesicles

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

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Supramolecule #1: Stripped Gas vesicles

SupramoleculeName: Stripped 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
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5 / Details: 10 mM HEPES, pH 7.5
VitrificationCryogen name: ETHANE-PROPANE

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 73866
ExtractionNumber tomograms: 23 / Number images used: 28887
Final angle assignmentType: ANGULAR RECONSTITUTION

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