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- EMDB-37738: In situ PBS from cyanobacterial Spirulina platensis -

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Basic information

Entry
Database: EMDB / ID: EMD-37738
TitleIn situ PBS from cyanobacterial Spirulina platensis
Map data
Sample
  • Cell: In situ PBS-PSII supercomplex from Spirulina platensis.
KeywordsPBS / PHOTOSYNTHESIS
Biological speciesArthrospira platensis FACHB-439 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYou X / Zhang X / Xiao YN / Sun S / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: In situ structure of PBS from Spirulina platensis.
Authors: You X / Zhang X / Xiao YN / Sui SF
History
DepositionOct 11, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37738.png

Downloads & links

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Map

FileDownload / File: emd_37738.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-1.1154456 - 1.5860527
Average (Standard dev.)0.006879584 (±0.072040215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 417.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37738_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37738_half_map_2.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 : In situ PBS-PSII supercomplex from Spirulina platensis.

EntireName: In situ PBS-PSII supercomplex from Spirulina platensis.
Components
  • Cell: In situ PBS-PSII supercomplex from Spirulina platensis.

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Supramolecule #1: In situ PBS-PSII supercomplex from Spirulina platensis.

SupramoleculeName: In situ PBS-PSII supercomplex from Spirulina platensis.
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#21, #23-#26, #28, #27, #29-#32, #22
Source (natural)Organism: Arthrospira platensis FACHB-439 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kgx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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