Pseudo-atomic model of gas vesicles

This pseudo-atomic model is shown in our recent 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)

(Update 26.04.2023), Now in:

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)

We use the atomic model from our determined 3.2 Å cryo-EM structure of the B.megaterium gas vesicle (GV) wall and copy+place it on a helical path that narrows at the tips of the GVs. Placement at the seam in the GV center is informed by high-resolution 2D class averages. The helical arrangement is informed by the determined helical symmetry of this particular helical polymorph (92.93 units per helical turn) and the tip by measurement of the cone semi-angle.

The pseudo-atomic model consists only of copies of the wall protein GvpA2. This is likely a simplification, and the homologous proteins GvpJ and GvpS might be involved in small parts of the assembly, such as the ends of the cones. The arrangement at the contact point of the two GV halves is informed only by high-resolution 2D data, therefore the 3D arrangement of these features is hypothetical.

For display in ChimeraX I recommend this style:

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

The rainbow color scheme highlighting the main chain can be displayed:

select :2-13; color sel #2c2a70; select :14-23; color sel #45639a; select :24-34; color sel #98b45a; select :35-39; color sel #abb24e; select :40-50; color sel #dddb20; select :51-61; color sel #e15a3d; select :62-66; color sel #ec1e24; ~sel;

The color scheme for physico-chemical properties:

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;

Python dictionary with color scheme:

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

To highlight both halves in different colors in the full model:

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

ChimeraX command to impose helical symmetry on a single GvpA monomer:

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