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- EMDB-18306: Towards the Visual Proteomics of C. reinhardtii using High-throug... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-18306
TitleTowards the Visual Proteomics of C. reinhardtii using High-throughput Collaborative in situ Cryo-ET : Representative Tomogram
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
KeywordsChlamydomonas reinhardtii cryo-Plasma-FIB / PHOTOSYNTHESIS
Biological speciesChlamydomonas reinhardtii (plant)
Methodelectron tomography / cryo EM
AuthorsKhavnekar S / Kelley R / Zhang X / Kotecha A
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
Other private
CitationJournal: Microsc Microanal / Year: 2023
Title: Towards the Visual Proteomics of C. reinhardtii using High-throughput Collaborative in situ Cryo-ET.
Authors: Sagar Khavnekar / Ron Kelley / Florent Waltz / Wojciech Wietrzynski / Xianjun Zhang / Martin Obr / Grigory Tagiltsev / Florian Beck / William Wan / John Briggs / Ben Engel / Juergen Plitzko / Abhay Kotecha /
History
DepositionAug 24, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18306.png

Downloads & links

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Map

FileDownload / File: emd_18306.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.84 Å/pix.
x 512 pix.
= 4014.08 Å		7.84 Å/pix.
x 1024 pix.
= 8028.16 Å		7.84 Å/pix.
x 1024 pix.
= 8028.16 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: 7.84 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2738.158199999999852 - 1448.254599999999982
Average (Standard dev.)11.466737999999999 (±22.968359)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024512
Spacing10241024512
CellA: 8028.16 Å / B: 8028.16 Å / C: 4014.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Chlamydomonas reinhardtii

EntireName: Chlamydomonas reinhardtii (plant)
Components
  • Cell: Chlamydomonas reinhardtii

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Supramolecule #1: Chlamydomonas reinhardtii

SupramoleculeName: Chlamydomonas reinhardtii / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 mat3-4 mt+

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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
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 12 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 120 / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 500 / Focused ion beam - Final thickness: 90
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Arctis. 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: FEI FALCON IV (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 1

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