8GBS | pdb_00008gbs

Integrative model of the native Ana GV shell

• PDB DOI: https://doi.org/10.2210/pdb8GBS/pdb
• EM Map EMD-29921: EMDB EMDataResource

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Dolichospermum flos-aquae
• Mutation(s): No 


• Deposited: 2023-02-28 Released: 2023-04-19 
• Deposition Author(s): 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 Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: TOMOGRAPHY 

Starting Model: experimental

Literature

Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET.

Dutka, P., Metskas, L.A., Hurt, R.C., Salahshoor, H., Wang, T.Y., Malounda, D., Lu, G.J., Chou, T.F., Shapiro, M.G., Jensen, G.J.

(2023) Structure 31: 518-528.e6

• PubMed: 37040766 
• DOI: https://doi.org/10.1016/j.str.2023.03.011
• Primary Citation Related Structures: 
  8GBS


• PubMed 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 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.

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Organizational Affiliation: 
• Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA. Electronic address: [e-mail].
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT 84602, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 32.97 kDa 
• Atom Count: 2,121 
• Modeled Residue Count: 293 
• Deposited Residue Count: 317 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gas vesicle structural protein	A [auth A1], B [auth A2], C [auth A4], E [auth A3]	71	Dolichospermum flos-aquae	Mutation(s): 0
UniProt
Find proteins for P10397 (Dolichospermum flosaquae) Explore P10397  Go to UniProtKB:  P10397

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gas vesicle protein C	D [auth C]	33	Dolichospermum flos-aquae	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: TOMOGRAPHY 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI127401
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	EB018975

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2023-04-26
  Changes: Database references
• Version 1.2: 2023-05-17
  Changes: Database references
• Version 1.3: 2024-06-19
  Changes: Data collection, Refinement description