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- EMDB-37747: In situ PSII dimer from cyanobacterial Spirulina platensis -

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Basic information

Entry
Database: EMDB / ID: EMD-37747
TitleIn situ PSII dimer from cyanobacterial Spirulina platensis
Map data
Sample
  • Cell: In situ PSII dimer from Spirulina platensis.
KeywordsPBS / PHOTOSYNTHESIS
Biological speciesArthrospira platensis FACHB-439 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYou X / Zhang X / Xiao YN / Sun S / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: In situ structural determination of cyanobacterial phycobilisome-PSII supercomplex by STAgSPA strategy.
Authors: Xing Zhang / Yanan Xiao / Xin You / Shan Sun / Sen-Fang Sui /
Abstract: Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) ...Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) and transferred to photosynthetic reaction centers of photosystem II (PSII) and photosystem I (PSI). While most of the protein complexes involved in photosynthesis have been characterized by in vitro structural analyses, how these protein complexes function together in vivo is not well understood. Here we implemented STAgSPA, an in situ structural analysis strategy, to solve the native structure of PBS-PSII supercomplex from the cyanobacteria Arthrospira sp. FACHB439 at resolution of ~3.5 Å. The structure reveals coupling details among adjacent PBSs and PSII dimers, and the collaborative energy transfer mechanism mediated by multiple super-PBS in cyanobacteria. Our results provide insights into the diversity of photosynthesis-related systems between prokaryotic cyanobacteria and eukaryotic red algae but are also a methodological demonstration for high-resolution structural analysis in cellular or tissue samples.
History
DepositionOct 11, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37747.png

Downloads & links

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Map

FileDownload / File: emd_37747.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.407
Minimum - Maximum-1.5485704 - 1.8775585
Average (Standard dev.)0.0015831041 (±0.077270724)
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_37747_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_37747_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : In situ PSII dimer from Spirulina platensis.

EntireName: In situ PSII dimer from Spirulina platensis.
Components
  • Cell: In situ PSII dimer from Spirulina platensis.

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Supramolecule #1: In situ PSII dimer from Spirulina platensis.

SupramoleculeName: In situ PSII dimer 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kgx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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