[English] 日本語
- EMDB-13756: P. carterae Golgi cisterna with forming coccolithosomes -

Open data

ID or keywords:


Basic information

Database: EMDB / ID: EMD-13756
TitleP. carterae Golgi cisterna with forming coccolithosomes
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.
DepositionOct 19, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBe / Status: Released

Structure visualization

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

Downloads & links


FileDownload / File: emd_13756.map.gz / Format: CCP4 / Size: 821.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

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


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
Minimum - Maximum-233.0 - 124.0
Average (Standard dev.)1.3716227 (±9.691508)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
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
MAP C/R/S123
start NC/NR/NS11250
D min/max/mean-233.000124.0001.372

Supplemental data

Sample components

Entire Pleurochrysis carterae

EntireName: Pleurochrysis carterae / Number of Components: 1

Component #1: cellular-component, Pleurochrysis carterae

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

Experimental details

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

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
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

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

About Yorodumi


Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more