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- PDB-8j7b: Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8j7b | ||||||
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Title | Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 2 (PSI-ST2) | ||||||
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![]() | PHOTOSYNTHESIS / photosystem / PLANT PROTEIN | ||||||
Function / homology | ![]() photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / chloroplast membrane / response to high light intensity / chloroplast thylakoid / plastoglobule / photosynthesis, light harvesting in photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / chloroplast membrane / response to high light intensity / chloroplast thylakoid / plastoglobule / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å | ||||||
![]() | Chen, S.J.B. / Wu, J.H. / Sui, S.F. / Zhang, L.X. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 889.7 KB | Display | ![]() |
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PDB format | ![]() | 768.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 10.5 MB | Display | ![]() |
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Full document | ![]() | 10.8 MB | Display | |
Data in XML | ![]() | 158.7 KB | Display | |
Data in CIF | ![]() | 201.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36037MC ![]() 8j6zC ![]() 8j7aC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Chlorophyll a-b binding protein ... , 2 types, 2 molecules 14
#1: Protein | Mass: 26021.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein | Mass: 27760.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Photosystem I chlorophyll a/b-binding protein ... , 2 types, 2 molecules 23
#2: Protein | Mass: 27782.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Protein | Mass: 29206.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#5: Protein | Mass: 83315.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#6: Protein | Mass: 82555.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL
#8: Protein | Mass: 22336.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#9: Protein | Mass: 14984.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#10: Protein | Mass: 24203.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#11: Protein | Mass: 17103.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#12: Protein | Mass: 15291.522 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#13: Protein/peptide | Mass: 4137.024 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#14: Protein/peptide | Mass: 5011.897 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#15: Protein | Mass: 13219.431 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#16: Protein | Mass: 23070.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules C![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#27: Sugar | ChemComp-DGD / |
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#7: Protein | Mass: 9049.509 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 10 types, 200 molecules ![](data/chem/img/CHL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL0.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL0.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
#17: Chemical | ChemComp-CHL / #18: Chemical | ChemComp-CLA / #19: Chemical | #20: Chemical | ChemComp-LHG / #21: Chemical | ChemComp-LUT / ( #22: Chemical | ChemComp-BCR / #23: Chemical | #24: Chemical | ChemComp-CL0 / | #25: Chemical | #26: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2) Type: COMPLEX / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137602 / Symmetry type: POINT | ||||||||||||||||||||||||
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