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- EMDB-12749: In situ cryo-electron tomogram of a pyrenoid inside a Chlamydomon... -

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Basic information

Entry
Database: EMDB / ID: EMD-12749
TitleIn situ cryo-electron tomogram of a pyrenoid inside a Chlamydomonas reinhardtii cell
Map dataIn situ cryo-electron tomogram of a pyrenoid inside a Chlamydomonas reinhardtii cell (bin4). A denoised version of this tomogram is included in the bundle.
Sample
  • Organelle or cellular component: Pyrenoid
Biological speciesChlamydomonas reinhardtii (plant)
Methodelectron tomography / cryo EM
AuthorsCuellar LK / Schaffer M / Strauss M / Martinez-Sanchez A / Plitzko JM / Foerster F / Engel BD
Funding support Germany, 2 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)FO 716/4-1 Germany
CitationJournal: Cell / Year: 2017
Title: The Eukaryotic CO-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization.
Authors: Elizabeth S Freeman Rosenzweig / Bin Xu / Luis Kuhn Cuellar / Antonio Martinez-Sanchez / Miroslava Schaffer / Mike Strauss / Heather N Cartwright / Pierre Ronceray / Jürgen M Plitzko / ...Authors: Elizabeth S Freeman Rosenzweig / Bin Xu / Luis Kuhn Cuellar / Antonio Martinez-Sanchez / Miroslava Schaffer / Mike Strauss / Heather N Cartwright / Pierre Ronceray / Jürgen M Plitzko / Friedrich Förster / Ned S Wingreen / Benjamin D Engel / Luke C M Mackinder / Martin C Jonikas /
Abstract: Approximately 30%-40% of global CO fixation occurs inside a non-membrane-bound organelle called the pyrenoid, which is found within the chloroplasts of most eukaryotic algae. The pyrenoid matrix is ...Approximately 30%-40% of global CO fixation occurs inside a non-membrane-bound organelle called the pyrenoid, which is found within the chloroplasts of most eukaryotic algae. The pyrenoid matrix is densely packed with the CO-fixing enzyme Rubisco and is thought to be a crystalline or amorphous solid. Here, we show that the pyrenoid matrix of the unicellular alga Chlamydomonas reinhardtii is not crystalline but behaves as a liquid that dissolves and condenses during cell division. Furthermore, we show that new pyrenoids are formed both by fission and de novo assembly. Our modeling predicts the existence of a "magic number" effect associated with special, highly stable heterocomplexes that influences phase separation in liquid-like organelles. This view of the pyrenoid matrix as a phase-separated compartment provides a paradigm for understanding its structure, biogenesis, and regulation. More broadly, our findings expand our understanding of the principles that govern the architecture and inheritance of liquid-like organelles.
History
DepositionApr 13, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 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
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

emd_12749.png

Downloads & links

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Map

FileDownload / File: emd_12749.map.gz / Format: CCP4 / Size: 762.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationIn situ cryo-electron tomogram of a pyrenoid inside a Chlamydomonas reinhardtii cell (bin4). A denoised version of this tomogram is included in the bundle.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.68 Å/pix.
x 464 pix.
= 6347.52 Å		13.68 Å/pix.
x 928 pix.
= 12695.04 Å		13.68 Å/pix.
x 928 pix.
= 12695.04 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: 13.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-92.0 - 66.0
Average (Standard dev.)2.2878852 (±9.710536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00232
Dimensions928928464
Spacing928928464
CellA: 12695.04 Å / B: 12695.04 Å / C: 6347.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z13.6813.6813.68
M x/y/z928928464
origin x/y/z0.0000.0000.000
length x/y/z12695.04012695.0406347.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS00232
NC/NR/NS928928464
D min/max/mean-92.00066.0002.288

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Supplemental data

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Additional map: Denoised tomogram by deconvolving with an ad-hoc Wiener filter.

Fileemd_12749_additional_1.map
AnnotationDenoised tomogram by deconvolving with an ad-hoc Wiener filter.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pyrenoid

EntireName: Pyrenoid
Components
  • Organelle or cellular component: Pyrenoid

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Supramolecule #1: Pyrenoid

SupramoleculeName: Pyrenoid / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.03 nA / Focused ion beam - Duration: 1800 sec. / Focused ion beam - Temperature: 91 K / Focused ion beam - Initial thickness: 8000 nm / Focused ion beam - Final thickness: 300 nm
Focused ion beam - Details: See https://bio-protocol.org/e1575 for detailed procedure.. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Quanta FIB. This is not in a list of ...Focused ion beam - Details: See https://bio-protocol.org/e1575 for detailed procedure.. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Quanta FIB. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 65

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