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- PDB-8gbs: Integrative model of the native Ana GV shell -

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Basic information

Entry
Database: PDB / ID: 8gbs
TitleIntegrative model of the native Ana GV shell
Components
  • Gas vesicle protein C
  • Gas vesicle structural protein
KeywordsCYTOSOLIC PROTEIN / Gas vesicles / Flotation / cyanobacteria
Function / homology
Function and homology information


gas vesicle shell / vesicle membrane / vacuole / 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 structural protein
Similarity search - Component
Biological speciesDolichospermum flos-aquae (bacteria)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 8 Å
AuthorsDutka, 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
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Gas vesicle structural protein
A2: Gas vesicle structural protein
A4: Gas vesicle structural protein
C: Gas vesicle protein C
A3: Gas vesicle structural protein


Theoretical massNumber of molelcules
Total (without water)32,9655
Polymers32,9655
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gas vesicle structural protein / GVP / Gas vesicle structural protein A / GvpA


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 Gas vesicle protein C / / Gas vesicle structural protein C / GvpC


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: Gas vesicles (GVs) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Dolichospermum flos-aquae (bacteria)
Buffer solutionpH: 7.5 / Details: 10 mM HEPES, pH 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 3, blot time 4 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.5/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameCategory
1SerialEMimage acquisition
6UCSF ChimeraXmodel fitting
8Warpseries alignment
9RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5874
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross-correlation, occupancy
Atomic model buildingPDB-ID: 7R1C

7r1c


Accession code: 7R1C / Source name: PDB / Type: experimental model

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