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Open data
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Basic information
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Title | Cryo-EM structure of Bacillus megaterium gas vesicles | |||||||||
![]() | Main map, automatically B-factor sharpened with -30 A**2 in cryoSPARC / symmetrized with -3.874 degree rotation, 0.525 A rise | |||||||||
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Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Huber ST / Evers W / Jakobi AJ | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Cryo-EM structure of gas vesicles for buoyancy-controlled motility. Authors: Stefan T Huber / Dion Terwiel / Wiel H Evers / David Maresca / Arjen J Jakobi / ![]() Abstract: Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, ...Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, we report the 3.2 Å cryo-EM structure of the gas vesicle shell made from the structural protein GvpA that self-assembles into hollow helical cylinders closed off by cone-shaped tips. Two helical half shells connect through a characteristic arrangement of GvpA monomers, suggesting a mechanism of gas vesicle biogenesis. The fold of GvpA features a corrugated wall structure typical for force-bearing thin-walled cylinders. Small pores enable gas molecules to diffuse across the shell, while the exceptionally hydrophobic interior surface effectively repels water. Comparative structural analysis confirms the evolutionary conservation of gas vesicle assemblies and demonstrates molecular features of shell reinforcement by GvpC. Our findings will further research into gas vesicle biology and facilitate molecular engineering of gas vesicles for ultrasound imaging. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 115.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.7 KB | Display | ![]() |
Images | ![]() | 245.5 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() ![]() | 115.5 MB 475.4 MB 475.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 892.9 KB | Display | ![]() |
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Full document | ![]() | 892.5 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Main map, automatically B-factor sharpened with -30 A**2 in cryoSPARC / symmetrized with -3.874 degree rotation, 0.525 A rise | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Unsharpened map / symmetrized with -3.874 degree rotation,...
File | emd_14340_additional_1.map | ||||||||||||
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Annotation | Unsharpened map / symmetrized with -3.874 degree rotation, 0.525 A rise | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A
File | emd_14340_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_14340_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Helical assembly of GvpB monomers forming the gas vesicle wall
Entire | Name: Helical assembly of GvpB monomers forming the gas vesicle wall |
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Components |
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-Supramolecule #1: Helical assembly of GvpB monomers forming the gas vesicle wall
Supramolecule | Name: Helical assembly of GvpB monomers forming the gas vesicle wall type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 9.99 MDa |
-Macromolecule #1: GvpA2/B from B.megaterium
Macromolecule | Name: GvpA2/B from B.megaterium / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSIQKSTNSS SLAEVIDRI L DKGIVIDA FA RVSVVGI EIL TIEARV VIAS VDTWL RYAEA VGLL RDDVEE NGL PERSNSS EG QPRFSI |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.45 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA PLUNGER / Details: Blot times between 5 and 11 seconds.. | |||||||||
Details | Concentration measured by OD(500)=3.12 against a sonicated blank. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4351 / Average exposure time: 2.4 sec. / Average electron dose: 30.0 e/Å2 Details: One shot per hole 1.37 A/pix 60 fractions over 30 e-/A2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.25 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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