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- EMDB-51427: Tomogram of pyrenoid of T. pseudonana -

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Basic information

Entry
Database: EMDB / ID: EMD-51427
TitleTomogram of pyrenoid of T. pseudonana
Map data
Sample
  • Cell: T. pseudonana shell4 KO
Keywordspyrenoid / rubisco / protein shell / carbon fixation / chloroplast / marine diatom / PHOTOSYNTHESIS
Biological speciesT. pseudonana (Diatom)
Methodelectron tomography / cryo EM
AuthorsDemulder M / Engel B
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)M822.00045European Union
CitationJournal: Cell / Year: 2024
Title: A protein blueprint of the diatom CO-fixing organelle.
Authors: Onyou Nam / Sabina Musiał / Manon Demulder / Caroline McKenzie / Adam Dowle / Matthew Dowson / James Barrett / James N Blaza / Benjamin D Engel / Luke C M Mackinder /
Abstract: Diatoms are central to the global carbon cycle. At the heart of diatom carbon fixation is an overlooked organelle called the pyrenoid, where concentrated CO is delivered to densely packed Rubisco. ...Diatoms are central to the global carbon cycle. At the heart of diatom carbon fixation is an overlooked organelle called the pyrenoid, where concentrated CO is delivered to densely packed Rubisco. Diatom pyrenoids fix approximately one-fifth of global CO, but the protein composition of this organelle is largely unknown. Using fluorescence protein tagging and affinity purification-mass spectrometry, we generate a high-confidence spatially defined protein-protein interaction network for the diatom pyrenoid. Within our pyrenoid interaction network are 10 proteins with previously unknown functions. We show that six of these form a shell that encapsulates the Rubisco matrix and is critical for pyrenoid structural integrity, shape, and function. Although not conserved at a sequence or structural level, the diatom pyrenoid shares some architectural similarities to prokaryotic carboxysomes. Collectively, our results support the convergent evolution of pyrenoids across the two main plastid lineages and uncover a major structural and functional component of global CO fixation.
History
DepositionAug 25, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51427.png

Downloads & links

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Map

FileDownload / File: emd_51427.map.gz / Format: CCP4 / Size: 2.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.57 Å/pix.
x 512 pix.
= 4388.864 Å		8.57 Å/pix.
x 1440 pix.
= 12343.68 Å		8.57 Å/pix.
x 1024 pix.
= 8777.728 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: 8.572 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.43477285 - 0.42933127
Average (Standard dev.)0.0062763896 (±0.062185317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208208-256
Dimensions14401024512
Spacing10241440512
CellA: 8777.728 Å / B: 12343.68 Å / C: 4388.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_51427_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T. pseudonana shell4 KO

EntireName: T. pseudonana shell4 KO
Components
  • Cell: T. pseudonana shell4 KO

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Supramolecule #1: T. pseudonana shell4 KO

SupramoleculeName: T. pseudonana shell4 KO / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: T. pseudonana (Diatom)

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 20 / Focused ion beam - Duration: 1 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.003 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 57

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