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- EMDB-13757: P. carterae coccolith vesicle with mature base plate -

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Basic information

Entry
Database: EMDB / ID: EMD-13757
TitleP. carterae coccolith vesicle with mature base plate
Map data
SamplePleurochrysis carterae
Biological speciesChrysotila carterae (eukaryote)
Methodelectron tomography / cryo EM
AuthorsKadan Y / Mahamid J / Gal A / Tollervey F
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
Israel Science Foundation697/19European Union
European Research Council (ERC)760067European Union
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Intracellular nanoscale architecture as a master regulator of calcium carbonate crystallization in marine microalgae.
Authors: Yuval Kadan / Fergus Tollervey / Neta Varsano / Julia Mahamid / Assaf Gal /
Abstract: Unicellular marine microalgae are responsible for one of the largest carbon sinks on Earth. This is in part due to intracellular formation of calcium carbonate scales termed coccoliths. ...Unicellular marine microalgae are responsible for one of the largest carbon sinks on Earth. This is in part due to intracellular formation of calcium carbonate scales termed coccoliths. Traditionally, the influence of changing environmental conditions on this process has been estimated using poorly constrained analogies to crystallization mechanisms in bulk solution, yielding ambiguous predictions. Here, we elucidated the intracellular nanoscale environment of coccolith formation in the model species using cryoelectron tomography. By visualizing cells at various stages of the crystallization process, we reconstructed a timeline of coccolith development. The three-dimensional data portray the native-state structural details of coccolith formation, uncovering the crystallization mechanism, and how it is spatially and temporally controlled. Most strikingly, the developing crystals are only tens of nanometers away from delimiting membranes, resulting in a highly confined volume for crystal growth. We calculate that the number of soluble ions that can be found in such a minute volume at any given time point is less than the number needed to allow the growth of a single atomic layer of the crystal and that the uptake of single protons can markedly affect nominal pH values. In such extreme confinement, the crystallization process is expected to depend primarily on the regulation of ion fluxes by the living cell, and nominal ion concentrations, such as pH, become the result, rather than a driver, of the crystallization process. These findings call for a new perspective on coccolith formation that does not rely exclusively on solution chemistry.
History
DepositionOct 19, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBe / Status: Released

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Structure visualization

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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_13757.map.gz / Format: CCP4 / Size: 821.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.48 Å/pix.
x 500 pix.
= 6740. Å
13.48 Å/pix.
x 928 pix.
= 12509.439 Å
13.48 Å/pix.
x 928 pix.
= 12509.439 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.48 Å
Density
Minimum - Maximum-90.0 - 97.0
Average (Standard dev.)1.4516227 (±9.2594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin221000
Dimensions928928500
Spacing928928500
CellA: 12509.439 Å / B: 12509.439 Å / C: 6740.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z13.47999892241413.47999892241413.48
M x/y/z928928500
origin x/y/z0.0000.0000.000
length x/y/z12509.43912509.4396740.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS221000
NC/NR/NS928928500
D min/max/mean-90.00097.0001.452

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Supplemental data

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Sample components

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Entire Pleurochrysis carterae

EntireName: Pleurochrysis carterae / Number of Components: 1

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Component #1: cellular-component, Pleurochrysis carterae

Cellular-componentName: Pleurochrysis carterae / Recombinant expression: No
SourceSpecies: Chrysotila carterae (eukaryote)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Cell / Method: cryo EM
Sample solutionBuffer solution: Sterile artificial seawater, supplemented with an f/2 nutrient recipe
pH: 8
Support film15 mA current
VitrificationInstrument: LEICA EM GP / Cryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 2.24 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 42000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Energy Filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of Sections: 51
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD

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