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- EMDB-14238: Cryo-EM structure of Bacillus megaterium gas vesicles -

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Basic information

Entry
Database: EMDB / ID: EMD-14238
TitleCryo-EM structure of Bacillus megaterium gas vesicles
Map dataSharpened cryo-EM density - cut to 128px box size around the part optimized in local refinement
Sample
  • Complex: Helical assembly of GvpB monomers forming the gas vesicle wall
    • Protein or peptide: Gas vesicle structural protein
Function / homology
Function and homology information


gas vesicle shell / vesicle membrane / vacuole / structural molecule activity
Similarity search - Function
Gas vesicle protein GvpA / Gas vesicle protein GvpA, conserved site / Gas vesicle protein / Gas vesicles protein GVPa signature 1. / Gas vesicles protein GVPa signature 2.
Similarity search - Domain/homology
Gas vesicle structural protein
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHuber ST / Evers W / Jakobi AJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Cell / Year: 2023
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.
#1: Journal: Biorxiv / Year: 2022
Title: Cryo-EM structure of gas vesicles for buoyancy-controlled motility
Authors: Huber ST / Terwiel D / Evers WH / Maresca D / Jakobi AJ
History
DepositionFeb 2, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14238.png

Downloads & links

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Map

FileDownload / File: emd_14238.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM density - cut to 128px box size around the part optimized in local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 128 pix.
= 175.36 Å		1.37 Å/pix.
x 128 pix.
= 175.36 Å		1.37 Å/pix.
x 128 pix.
= 175.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.665342 - 5.205916
Average (Standard dev.)-0.010282499 (±0.44117287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-187-54
Dimensions128128128
Spacing128128128
CellA=B=C: 175.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14238_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Symmetrized cryo-EM density before local refinement / helical...

Fileemd_14238_additional_1.map
AnnotationSymmetrized cryo-EM density before local refinement / helical twist is -3.874 degrees / helical rise is 0.525 Angstroms.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened cryo-EM density - cut to 128px box...

Fileemd_14238_additional_2.map
AnnotationUnsharpened cryo-EM density - cut to 128px box size around the part optimized in local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B - cut to 128px box size...

Fileemd_14238_half_map_1.map
AnnotationHalf-map B - cut to 128px box size around the part optimized in local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A - cut to 128px box size...

Fileemd_14238_half_map_2.map
AnnotationHalf-map A - cut to 128px box size around the part optimized in local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical assembly of GvpB monomers forming the gas vesicle wall

EntireName: Helical assembly of GvpB monomers forming the gas vesicle wall
Components
  • Complex: Helical assembly of GvpB monomers forming the gas vesicle wall
    • Protein or peptide: Gas vesicle structural protein

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Supramolecule #1: Helical assembly of GvpB monomers forming the gas vesicle wall

SupramoleculeName: Helical assembly of GvpB monomers forming the gas vesicle wall
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Molecular weightTheoretical: 9.99 MDa

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Macromolecule #1: Gas vesicle structural protein

MacromoleculeName: Gas vesicle structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Strain: ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512
Molecular weightTheoretical: 9.62685 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSIQKSTNSS SLAEVIDRIL DKGIVIDAFA RVSVVGIEIL TIEARVVIAS VDTWLRYAEA VGLLRDDVEE NGLPERSNSS EGQPRFSI

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.45 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-Cltris(hydroxymethyl)aminomethane
50.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA PLUNGER / Details: Blot times between 5 and 11 seconds..
DetailsConcentration measured by OD(500)=3.12 against a sonicated blank.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.25 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 36295 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: INSILICO MODEL / In silico model: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.3)
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 0.525 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.874 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3)
Details: Final reconstruction in cryoSPARC 3.3 using local refinement in a small section of the cylinder
Number images used: 1460
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7r1c:
Cryo-EM structure of Bacillus megaterium gas vesicles

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