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- PDB-8hg5: Cryo-EM structure of the prasinophyte-specific light-harvesting c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hg5 | |||||||||||||||
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Title | Cryo-EM structure of the prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri | |||||||||||||||
![]() | (Chlorophyll a-b binding protein, ...) x 2 | |||||||||||||||
![]() | ELECTRON TRANSPORT / Complex / Light-harvesting / Photosynthesis | |||||||||||||||
Function / homology | ![]() photosynthesis, light harvesting in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
![]() | Shan, J. / Sheng, X. / Ishii, A. / Watanabe, A. / Song, C. / Murata, K. / Minagawa, J. / Liu, Z. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The photosystem I supercomplex from a primordial green alga harbors three light-harvesting complex trimers. Authors: Asako Ishii / Jianyu Shan / Xin Sheng / Eunchul Kim / Akimasa Watanabe / Makio Yokono / Chiyo Noda / Chihong Song / Kazuyoshi Murata / Zhenfeng Liu / Jun Minagawa / ![]() ![]() Abstract: As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in ...As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of PSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll 603-609 pair in Lhca1-4. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 201.3 KB | Display | ![]() |
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PDB format | ![]() | 181.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34735MC ![]() 7ycaC ![]() 8hg3C ![]() 8hg6C 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, 3 molecules PRQ
#1: Protein | Mass: 24689.807 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 24161.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 6 types, 63 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/KC2.gif)
![](data/chem/img/Q6L.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/IWJ.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/KC2.gif)
![](data/chem/img/Q6L.gif)
![](data/chem/img/NEX.gif)
![](data/chem/img/IWJ.gif)
#3: Chemical | ChemComp-CLA / #4: Chemical | ChemComp-CHL / #5: Chemical | #6: Chemical | ChemComp-Q6L / ( #7: Chemical | #8: Chemical | ChemComp-IWJ / ( |
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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 prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 defocus max: 2200 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80573 / Symmetry type: POINT |