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

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Basic information

Entry
Database: PDB / ID: 7r1c
TitleCryo-EM structure of Bacillus megaterium gas vesicles
ComponentsGas vesicle structural protein
KeywordsSTRUCTURAL PROTEIN / gas vesicle / buoyancy / helical / microbial motility
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHuber, S.T. / Evers, W. / Jakobi, A.J.
Funding support1items
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, S.T. / Terwiel, D. / Evers, W.H. / Maresca, D. / Jakobi, A.J.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: Gas vesicle structural protein


Theoretical massNumber of molelcules
Total (without water)9,6271
Polymers9,6271
Non-polymers00
Water0
1
N: Gas vesicle structural protein
x 5


Theoretical massNumber of molelcules
Total (without water)48,1345
Polymers48,1345
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
2
N: Gas vesicle structural protein
x 100


Theoretical massNumber of molelcules
Total (without water)962,685100
Polymers962,685100
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation99
3
N: Gas vesicle structural protein
x 930


Theoretical massNumber of molelcules
Total (without water)8,952,971930
Polymers8,952,971930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation929

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Components

#1: Protein Gas vesicle structural protein / GVP


Mass: 9626.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: gvpA, BG04_216, G3M54_29730 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: A0A0B6AAV2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical assembly of GvpB monomers forming the gas vesicle wall
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 9.99 MDa / Experimental value: NO
Source (natural)Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-DE3-pLysS
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethaneTris-Cl1
250 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Concentration measured by OD(500)=3.12 against a sonicated blank.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K / Details: Blot times between 5 and 11 seconds.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 64000 X / Nominal defocus max: 1250 nm / Nominal defocus min: 250 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4351
Details: One shot per hole 1.37 A/pix 60 fractions over 30 e-/A2
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
4RELION3.1CTF correction
10cryoSPARC3.3final Euler assignment
11RELION3.1classification
12cryoSPARC3.33D reconstruction
13PHENIX1.13model refinement
14ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.874 ° / Axial rise/subunit: 0.525 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 36295
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1460 / Algorithm: BACK PROJECTION
Details: Final reconstruction in cryoSPARC 3.3 using local refinement in a small section of the cylinder
Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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