+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29921 | |||||||||
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Title | Subtomogram average of the native Ana GV shell | |||||||||
Map data | native AnaGV map | |||||||||
Sample |
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Function / homology | Function and homology information gas vesicle shell / vesicle membrane / vacuole / structural molecule activity Similarity search - Function | |||||||||
Biological species | Dolichospermum flos-aquae (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Dutka 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
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29921.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-29921-v30.xml emd-29921.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_29921.png | 86.7 KB | ||
Masks | emd_29921_msk_1.map | 21.5 MB | Mask map | |
Others | emd_29921_half_map_1.map.gz emd_29921_half_map_2.map.gz | 15.9 MB 15.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29921 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29921 | HTTPS FTP |
-Validation report
Summary document | emd_29921_validation.pdf.gz | 722.6 KB | Display | EMDB validaton report |
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Full document | emd_29921_full_validation.pdf.gz | 722.1 KB | Display | |
Data in XML | emd_29921_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_29921_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29921 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29921 | HTTPS FTP |
-Related structure data
Related structure data | 8gbsMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29921.map.gz / Format: CCP4 / Size: 21.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | native AnaGV map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.687 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29921_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: native AnaGV halfmap1
File | emd_29921_half_map_1.map | ||||||||||||
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Annotation | native AnaGV halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: native AnaGV halfmap2
File | emd_29921_half_map_2.map | ||||||||||||
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Annotation | native AnaGV halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Stripped Gas vesicles
Entire | Name: Stripped Gas vesicles |
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Components |
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-Supramolecule #1: Stripped Gas vesicles
Supramolecule | Name: Stripped Gas vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Dolichospermum flos-aquae (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 / Details: 10 mM HEPES, pH 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 73866 |
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Extraction | Number tomograms: 23 / Number images used: 28887 |
Final angle assignment | Type: ANGULAR RECONSTITUTION |