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- EMDB-10868: stacked PSII-LHCII C2S2M2 supercomplexes from Pisum sativum grown... -

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Basic information

Entry
Database: EMDB / ID: EMD-10868
Titlestacked PSII-LHCII C2S2M2 supercomplexes from Pisum sativum grown in Low light conditions
Map data
Sample
  • Complex: PSII-LHCII C2S2 supercomplex
Biological speciesPisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.1 Å
AuthorsGrinzato A / Albanese P / Swuec P / Bolognesi M / Zanotti G / Pagliano C
CitationJournal: Int J Mol Sci / Year: 2020
Title: High-Light versus Low-Light: Effects on Paired Photosystem II Supercomplex Structural Rearrangement in Pea Plants.
Authors: Alessandro Grinzato / Pascal Albanese / Roberto Marotta / Paolo Swuec / Guido Saracco / Martino Bolognesi / Giuseppe Zanotti / Cristina Pagliano /
Abstract: In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is ...In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is dynamically adjusted in response to light cues, with the CS more abundant in high-light and the CSM in low-light. Paired PSII-LHCII supercomplexes interacting at their stromal surface from adjacent thylakoid membranes were previously suggested to mediate stacking. Here, we present the cryo-electron microscopy maps of paired CS and CSM supercomplexes isolated from pea plants grown in high-light and low-light, respectively. These maps show a different rotational offset between the two supercomplexes in the pair, responsible for modifying their reciprocal interaction and energetic connectivity. This evidence reveals a different way by which paired PSII-LHCII supercomplexes can mediate stacking at diverse irradiances. Electrostatic stromal interactions between LHCII trimers almost completely overlapping in the paired CS can be the main determinant by which PSII-LHCII supercomplexes mediate stacking in plants grown in high-light, whereas the mutual interaction of stromal N-terminal loops of two facing Lhcb4 subunits in the paired CSM can fulfil this task in plants grown in low-light. The high-light induced accumulation of the Lhcb4.3 protein in PSII-LHCII supercomplexes has been previously reported. Our cryo-electron microscopy map at 3.8 Å resolution of the CS supercomplex isolated from plants grown in high-light suggests the presence of the Lhcb4.3 protein revealing peculiar structural features of this high-light-specific antenna important for photoprotection.
History
DepositionApr 15, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.44
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10868.png

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Map

FileDownload / File: emd_10868.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.82 Å/pix.
x 240 pix.
= 436.8 Å		1.82 Å/pix.
x 240 pix.
= 436.8 Å		1.82 Å/pix.
x 240 pix.
= 436.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44 / Movie #1: 0.44
Minimum - Maximum-0.6688278 - 1.5829757
Average (Standard dev.)0.02487146 (±0.20792675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 436.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.821.821.82
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z436.800436.800436.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.6691.5830.025

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Supplemental data

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Sample components

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Entire : PSII-LHCII C2S2 supercomplex

EntireName: PSII-LHCII C2S2 supercomplex
Components
  • Complex: PSII-LHCII C2S2 supercomplex

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Supramolecule #1: PSII-LHCII C2S2 supercomplex

SupramoleculeName: PSII-LHCII C2S2 supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Pisum sativum (garden pea)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11094
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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