Cryo-EM structure of gas vesicles - supplementary data

This deposition contains supplementary data from our preprint:
Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D., & Jakobi, A. J. (2022). Cryo-EM structure of gas vesicles for buoyancy-controlled motility. bioRxiv, 2022-05.
(Update 26.04.2023), Now in:
Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D., & Jakobi, A. J. (2023). Cryo-EM structure of gas vesicles for buoyancy-controlled motility. Cell, 186(5), 975-986.

2Dclasses_AnaMega_SeamsEdgesWallTips.zip
This folder contains 2D class averages of different features of A.flos-aquae and B.megaterium gas vesicles (GVs) such as the seams between both GV halves, GV wall edges, collapsed walls and tips. We use this data to inform our pseudo-atomic model of an entire gas vesicle, and derive a model for biogenesis and growth. Some 2D classes provide high-resolution views on the GV wall in projection with a resolution that show the α-helical pitch and large side-chain densities. We use those views to confirm the evolutionarily conserved fold of the gas vesicle wall protein.
The box size and pixel size of the 2D classes is contained in the file names. A selected and sharpened 2D class for display in the manuscript is included in .png format.
AlphaFold2_Models_5merRib_DifferentOrganisms.zip
This folder contains five AlphaFold2 predictions of a single rib of the gas vesicle wall for organisms that are evolutionarily only little related (GvpA1 and GvpA2 from B.megaterium, GvpA from A.flos-aquae and GvpA1 and GvpA2 from H.salinarum). AF2 predicts very similar structure for these organisms, further supporting the high conservation of the gas vesicle wall.
AnaGvpA_GvpC_ComputationalDocking_HADDOCK.zip
In the manuscript, we propose a binding mode of the secondary protein GvpC to A.flos-aquae gas vesicles using computational docking with HADDOCK. We present two possible solutions with opposite orientation. The cif-files of the docking solution is contained in this folder.
GasPoreAnalysis.zip
We analysed gas pores between α-helix 1 of adjacent GvpA monomers using MOLE2.5. The three resulting tunnels are in this folder. The respective pdb files contain the constriction in Ångstrom in each line. A Chimera 1.13.1 session is included for visualisation.