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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 dataP. carterae coccolith vesicle with mature base plate
Sample
  • Cell: Pleurochrysis 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

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

emd_13757.png

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)
AnnotationP. carterae coccolith vesicle with mature base plate
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

Histogram

Histogram (log scale)
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
Components
  • Cell: Pleurochrysis carterae

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Supramolecule #1: Pleurochrysis carterae

SupramoleculeName: Pleurochrysis carterae / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chrysotila carterae (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 8
Details: Sterile artificial seawater, supplemented with an f/2 nutrient recipe
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa / Details: 15 mA current
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.05 nA / Focused ion beam - Duration: 1800 sec. / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 5000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: For details, see publication. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so ...Focused ion beam - Details: For details, see publication. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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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 magnification: 42000
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average exposure time: 1.6 sec. / Average electron dose: 2.24 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 51

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