DOI: 10.5281/zenodo.6458344
title: Pseudo-atomic model of a complete gas vesicle

description: Model construction

The model is generated by copying the atomic model built from our 3.2 Å cryo-EM reconstruction of the Bacillus megaterium gas vesicle wall and placing it along a helical trajectory that tapers toward the vesicle tips. Placement at the central seam is guided by high-resolution 2D class averages. The helical arrangement follows the experimentally determined symmetry of this helical polymorph, with 92.93 asymmetric units per helical turn, while the vesicle tips are modeled using the measured cone semi-angle.

Composition and limitations

The pseudo-atomic model consists exclusively of repeated copies of the wall protein GvpA2. This is likely a simplification, as the homologous proteins GvpJ and GvpS may contribute locally to the assembly, particularly at the conical tips. In addition, the arrangement at the junction between the two gas vesicle halves is constrained only by high-resolution 2D data. As a result, the precise three-dimensional organization in this region may deviate slightly from the true structure.

3D-printable model

A scaled, 3D-printable version of the model is available for educational and display purposes. The model is provided as two movable half-shells to illustrate the proposed growth mechanism at the central seam. For practical printing, each half-shell is subdivided into three parts and requires post-printing assembly using adhesive. GvpC molecules at realistic scale and with indications of the five 33 amino acid repeats can be printed and attached on the outside. At full scale (1:5,000,000), printing typically requires on the order of 120 hours and approximately 0.5 kg of filament. Files for a reduced 50 percent scale model are also included.



https://www.printables.com/model/189757-educational-model-gas-vesicle-scale-15000000


Visualization in ChimeraX

For visualization in ChimeraX, the following simplified protein cartoon style is recommended to reduce polygon count and make interactive visualization possible:



car style protein modeh default arrows f xsect oval width 3 thick 3 divisions 2 barSides 4


To display a rainbow color scheme along the protein sequence:



select :2-10; color sel #2c2a70; select :11-23; color sel #45639a; select :24-34; color sel #98b45a; select :35-37; color sel #abb24e; select :38-49; color sel #dddb20; select :50-62; color sel #e15a3d; select :63-66; color sel #ec1e24; ~sel;


Residues can alternatively be colored by physico-chemical property:



select :Met,Ile,Leu,Ala,Val; color sel #e1b13e; select :Ser,Thr,Gln,Asn; color sel #49c2c6; select :Glu,Asp; color sel #cb2026; select :Lys,Arg,His; color sel #3e58a8; select :Phe,Trp,Tyr; color sel #715321; select :Gly,Pro; color sel #7b7b7b; ~sel;


Corresponding Python dictionary:



colorscheme = {'#e1b13e':'MILAV', '#49c2c6':'STNQ', '#cb2026':'DE', '#3e58a8':'KRH', '#715321':'FYW', '#7b7b7b':'GPC'}


To visually distinguish the two halves of the full gas vesicle model:



color #1.1-865 gray; color #1.866-1730 steel blue


To generate the full assembly by imposing helical symmetry on a single GvpA monomer:



sym #1 h,0.5257,-3.87399,500,-250 coordinateSystem #1 copies True


Reference and Context

This pseudo-atomic model is presented in our cryo-EM study of gas vesicles, first published in the preprint:

Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D. & Jakobi, A. J. Cryo-EM structure of gas vesicles for buoyancy-controlled motility. BioRxiv (2022)

and subsequently peer-reviewed here:

Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D. & Jakobi, A. J. Cryo-EM structure of gas vesicles for buoyancy-controlled motility. Cell 186, 975–986 (2023)