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Open data
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Basic information
Entry | Database: PDB / ID: 8ix2 | |||||||||
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Title | Cryo-EM structure of unprotonated LHCII nanodisc at low pH value | |||||||||
![]() | Chlorophyll a-b binding protein, chloroplastic | |||||||||
![]() | PLANT PROTEIN / LHCII / Light-harvesting complex / Photosynthesis | |||||||||
Function / homology | ![]() plastoglobule / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.8 Å | |||||||||
![]() | Ruan, M.X. / Ding, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of LHCII in photo-active and photo-protecting states reveal allosteric regulation of light harvesting and excess energy dissipation. Authors: Meixia Ruan / Hao Li / Ying Zhang / Ruoqi Zhao / Jun Zhang / Yingjie Wang / Jiali Gao / Zhuan Wang / Yumei Wang / Dapeng Sun / Wei Ding / Yuxiang Weng / ![]() ![]() Abstract: The major light-harvesting complex of photosystem II (LHCII) has a dual regulatory function in a process called non-photochemical quenching to avoid the formation of reactive oxygen. LHCII undergoes ...The major light-harvesting complex of photosystem II (LHCII) has a dual regulatory function in a process called non-photochemical quenching to avoid the formation of reactive oxygen. LHCII undergoes reversible conformation transitions to switch between a light-harvesting state for excited-state energy transfer and an energy-quenching state for dissipating excess energy under full sunshine. Here we report cryo-electron microscopy structures of LHCII in membrane nanodiscs, which mimic in vivo LHCII, and in detergent solution at pH 7.8 and 5.4, respectively. We found that, under low pH conditions, the salt bridges at the lumenal side of LHCII are broken, accompanied by the formation of two local α-helices on the lumen side. The formation of α-helices in turn triggers allosterically global protein conformational change, resulting in a smaller crossing angle between transmembrane helices. The fluorescence decay rates corresponding to different conformational states follow the Dexter energy transfer mechanism with a characteristic transition distance of 5.6 Å between Lut1 and Chl612. The experimental observations are consistent with the computed electronic coupling strengths using multistate density function theory. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.7 KB | Display | ![]() |
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PDB format | ![]() | 187 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 35787MC ![]() 8iwxC ![]() 8iwyC ![]() 8iwzC ![]() 8ix0C ![]() 8ix1C 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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1 |
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Components
-Protein , 1 types, 3 molecules NGY
#1: Protein | Mass: 23497.549 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 6 types, 57 molecules ![](data/chem/img/CHL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LUT.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/XAT.gif)
#2: Chemical | ChemComp-CHL / #3: Chemical | ChemComp-CLA / #4: Chemical | ChemComp-LUT / ( #5: Chemical | #6: Chemical | #7: 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: LHCII nanodsic at low pH value / Type: COMPLEX / Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.12 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 5.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO / Details: This sample was monodisperse. | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 2500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Temperature (max): 80 K / Temperature (min): 70 K |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 11375 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353360 / Symmetry type: POINT |