+Open data
-Basic information
Entry | Database: PDB / ID: 8gbs | |||||||||
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Title | Integrative model of the native Ana GV shell | |||||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Gas vesicles / Flotation / cyanobacteria | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Dolichospermum flos-aquae (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 8 Å | |||||||||
Authors | Dutka, P. / Metskas, L.A. / Hurt, R.C. / Salahshoor, H. / Wang, T.U. / Malounda, D. / Lu, G. / Chou, T.F. / Shapiro, M.G. / Jensen, J.J. | |||||||||
Funding support | United States, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gbs.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gbs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8gbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/8gbs ftp://data.pdbj.org/pub/pdb/validation_reports/gb/8gbs | HTTPS FTP |
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-Related structure data
Related structure data | 29921MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 7534.721 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dolichospermum flos-aquae (bacteria) / References: UniProt: P10397 #2: Protein/peptide | | Mass: 2826.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dolichospermum flos-aquae (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: electron tomography |
-Sample preparation
Component | Name: Gas vesicles (GVs) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Dolichospermum flos-aquae (bacteria) |
Buffer solution | pH: 7.5 / Details: 10 mM HEPES, pH 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 3, blot time 4 s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.5/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | |||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||
3D reconstruction | Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5874 | |||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation, occupancy | |||||||||||||||
Atomic model building | PDB-ID: 7R1C Accession code: 7R1C / Source name: PDB / Type: experimental model |