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- EMDB-33669: In situ double-PBS-PSII-PSI-LHCs megacomplex from red alga Porphy... -

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Basic information

Entry
Database: EMDB / ID: EMD-33669
TitleIn situ double-PBS-PSII-PSI-LHCs megacomplex from red alga Porphyridium purpureum.
Map data
Sample
  • Cell: In situ PBS from Porphyridium purpureum
KeywordsDouble-PBS-PSII-PSI-LHCs / PHOTOSYNTHESIS
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYou X / Zhang X / Cheng J / Xiao YN / Sun S / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2023
Title: In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex.
Authors: Xin You / Xing Zhang / Jing Cheng / Yanan Xiao / Jianfei Ma / Shan Sun / Xinzheng Zhang / Hong-Wei Wang / Sen-Fang Sui /
Abstract: In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red ...In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red algae consist of soluble phycobilisomes (PBSs) and transmembrane light-harvesting complexes (LHCs). Excitation energy transfer pathways from PBS to photosystems remain unclear owing to the lack of structural information. Here we present in situ structures of PBS-PSII-PSI-LHC megacomplexes from the red alga Porphyridium purpureum at near-atomic resolution using cryogenic electron tomography and in situ single-particle analysis, providing interaction details between PBS, PSII and PSI. The structures reveal several unidentified and incomplete proteins and their roles in the assembly of the megacomplex, as well as a huge and sophisticated pigment network. This work provides a solid structural basis for unravelling the mechanisms of PBS-PSII-PSI-LHC megacomplex assembly, efficient energy transfer from PBS to the two photosystems, and regulation of energy distribution between PSII and PSI.
History
DepositionJun 22, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33669.png

Downloads & links

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Map

FileDownload / File: emd_33669.map.gz / Format: CCP4 / Size: 824 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 600 pix.
= 979.2 Å		1.63 Å/pix.
x 600 pix.
= 979.2 Å		1.63 Å/pix.
x 600 pix.
= 979.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.33669832 - 0.6392663
Average (Standard dev.)-0.001841121 (±0.047642466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 979.19995 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33669_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_33669_half_map_2.map
Projections & Slices
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Sample components

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Entire : In situ PBS from Porphyridium purpureum

EntireName: In situ PBS from Porphyridium purpureum
Components
  • Cell: In situ PBS from Porphyridium purpureum

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Supramolecule #1: In situ PBS from Porphyridium purpureum

SupramoleculeName: In situ PBS from Porphyridium purpureum / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#106
Source (natural)Organism: Porphyridium purpureum (eukaryote)

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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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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