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- EMDB-31246: Cryo-electron tomogram of phycobilisome-photosystem II supercompl... -

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Basic information

Entry
Database: EMDB / ID: EMD-31246
TitleCryo-electron tomogram of phycobilisome-photosystem II supercomplex on the thylakoid
Map dataCryo-electron tomogram of phycobilisome-photosystem II supercomplex on the thylakoid
Sample
  • Cell: phycobilisome-photosystem II supercomplex
Biological speciesPorphyridium purpureum (eukaryote)
Methodelectron tomography / cryo EM
AuthorsSui SF / Li XM / Li MJ / Ma JF
Funding support China, 4 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504600 China
National Basic Research Program of China (973 Program)2016YFA0501902 China
National Basic Research Program of China (973 Program)31861143048 China
National Basic Research Program of China (973 Program)31722015 China
CitationJournal: To Be Published
Title: In situ cryo-ET structure of phycobilisome-photosystem II supercomplex from red alga
Authors: Sui SF / Li XM / Li MJ / Ma JF
History
DepositionApr 26, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateMay 4, 2022-
Current statusMay 4, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31246.png

Downloads & links

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Map

FileDownload / File: emd_31246.map.gz / Format: CCP4 / Size: 535.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of phycobilisome-photosystem II supercomplex on the thylakoid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.68 Å/pix.
x 158 pix.
= 2162.072 Å		13.68 Å/pix.
x 927 pix.
= 12685.068 Å		13.68 Å/pix.
x 959 pix.
= 13122.956 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: 13.684 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.05200793 - 0.101698056
Average (Standard dev.)0.04112601 (±0.00972164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-353
Dimensions927959158
Spacing959927158
CellA: 13122.956 Å / B: 12685.068 Å / C: 2162.072 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : phycobilisome-photosystem II supercomplex

EntireName: phycobilisome-photosystem II supercomplex
Components
  • Cell: phycobilisome-photosystem II supercomplex

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Supramolecule #1: phycobilisome-photosystem II supercomplex

SupramoleculeName: phycobilisome-photosystem II supercomplex / type: cell / ID: 1 / Parent: 0 / Details: phycobilisome, photosystem II
Source (natural)Organism: Porphyridium purpureum (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: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 5 kV / Focused ion beam - Current: 0.1 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 191 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: 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 SUMMIT (4k x 4k) / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 42

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Atomic model buiding 1

Initial model(PDB ID:

6kgx

,

4yuu

)
RefinementProtocol: FLEXIBLE FIT

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