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- EMDB-36033: Cryo-EM structure of the Arabidopsis thaliana PSI in state 1 (PSI-ST1) -

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Basic information

Entry
Database: EMDB / ID: EMD-36033
TitleCryo-EM structure of the Arabidopsis thaliana PSI in state 1 (PSI-ST1)
Map data
Sample
  • Complex: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
Keywordsphotosystem / PLANT PROTEIN / PHOTOSYNTHESIS
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsChen SJB / Wu JH / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Plant / Year: 2023
Title: Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions.
Authors: Jianghao Wu / Shuaijiabin Chen / Chao Wang / Weijun Lin / Chao Huang / Chengxu Fan / Dexian Han / Dandan Lu / Xiumei Xu / SenFang Sui / Lixin Zhang /
Abstract: State transition is a fundamental light acclimation mechanism of photosynthetic organisms in response to the environmental light conditions. This process rebalances the excitation energy between ...State transition is a fundamental light acclimation mechanism of photosynthetic organisms in response to the environmental light conditions. This process rebalances the excitation energy between photosystem I (PSI) and photosystem II through regulated reversible binding of the light-harvesting complex II (LHCII) to PSI. However, the structural reorganization of PSI-LHCI, the dynamic binding of LHCII, and the regulatory mechanisms underlying state transitions are less understood in higher plants. In this study, using cryoelectron microscopy we resolved the structures of PSI-LHCI in both state 1 (PSI-LHCI-ST1) and state 2 (PSI-LHCI-LHCII-ST2) from Arabidopsis thaliana. Combined genetic and functional analyses revealed novel contacts between Lhcb1 and PsaK that further enhanced the binding of the LHCII trimer to the PSI core with the known interactions between phosphorylated Lhcb2 and the PsaL/PsaH/PsaO subunits. Specifically, PsaO was absent in the PSI-LHCI-ST1 supercomplex but present in the PSI-LHCI-LHCII-ST2 supercomplex, in which the PsaL/PsaK/PsaA subunits undergo several conformational changes to strengthen the binding of PsaO in ST2. Furthermore, the PSI-LHCI module adopts a more compact configuration with shorter Mg-to-Mg distances between the chlorophylls, which may enhance the energy transfer efficiency from the peripheral antenna to the PSI core in ST2. Collectively, our work provides novel structural and functional insights into the mechanisms of light acclimation during state transitions in higher plants.
History
DepositionApr 27, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36033.png

Downloads & links

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Map

FileDownload / File: emd_36033.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Contour LevelBy AUTHOR: 0.107
Minimum - Maximum-1.1102248 - 2.0467625
Average (Standard dev.)-0.0006271877 (±0.042119905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36033_msk_1.map
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Half map: #1

Fileemd_36033_half_map_1.map
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Half map: #2

Fileemd_36033_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-L...

EntireName: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
Components
  • Complex: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)

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Supramolecule #1: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-L...

SupramoleculeName: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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: 7.4
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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95589
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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