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- PDB-6ly5: Organization and energy transfer in a huge diatom PSI-FCPI superc... -
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Basic information
Entry | Database: PDB / ID: 6ly5 | ||||||
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Title | Organization and energy transfer in a huge diatom PSI-FCPI supercomplex | ||||||
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![]() | PHOTOSYNTHESIS / diatom / PSI-FCPI / photosysyem | ||||||
Function / homology | ![]() light-harvesting complex / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / photosystem I / plastid / chlorophyll binding ...light-harvesting complex / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å | ||||||
![]() | Xiong, P. / Caizhe, X. | ||||||
![]() | ![]() Title: Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex. Authors: Caizhe Xu / Xiong Pi / Yawen Huang / Guangye Han / Xiaobo Chen / Xiaochun Qin / Guoqiang Huang / Songhao Zhao / Yanyan Yang / Tingyun Kuang / Wenda Wang / Sen-Fang Sui / Jian-Ren Shen / ![]() ![]() Abstract: Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of ...Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of fucoxanthin-chlorophyll a/c proteins (FCPIs). We report the structure of PSI-FCPI from a diatom Chaetoceros gracilis at 2.38 Å resolution by single-particle cryo-electron microscopy. PSI-FCPI is a monomeric supercomplex consisting of 12 core and 24 antenna subunits (FCPIs), and 326 chlorophylls a, 34 chlorophylls c, 102 fucoxanthins, 35 diadinoxanthins, 18 β-carotenes and some electron transfer cofactors. Two subunits designated PsaR and PsaS were found in the core, whereas several subunits were lost. The large number of pigments constitute a unique and huge network ensuring efficient energy harvesting, transfer and dissipation. These results provide a firm structural basis for unraveling the mechanisms of light-energy harvesting, transfer and quenching in the diatom PSI-FCPI, and also important clues to evolutionary changes of PSI-LHCI. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.7 MB | Display | ![]() |
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PDB format | ![]() | 1.6 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 26 MB | Display | ![]() |
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Full document | ![]() | 27.7 MB | Display | |
Data in XML | ![]() | 471.4 KB | Display | |
Data in CIF | ![]() | 534 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30012MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Protein , 30 types, 33 molecules ABCDEFGHIJKLMNOPQRSTWXabcdeflg...
-Protein/peptide , 3 types, 3 molecules ijm
#26: Protein/peptide | Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#27: Protein/peptide | Mass: 4733.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#29: Protein/peptide | Mass: 3139.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 2 types, 29 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#39: Sugar | ChemComp-LMT / #40: Sugar | |
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-Non-polymers , 11 types, 713 molecules ![](data/chem/img/DD6.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/KC1.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/KC1.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
#34: Chemical | ChemComp-DD6 / ( #35: Chemical | ChemComp-A86 / ( #36: Chemical | ChemComp-CLA / #37: Chemical | ChemComp-KC1 / #38: Chemical | #41: Chemical | ChemComp-LHG / #42: Chemical | ChemComp-LMG / #43: Chemical | #44: Chemical | ChemComp-BCR / #45: Chemical | #46: Water | ChemComp-HOH / | |
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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: a huge diatom PSI-FCPI supercomplex / Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 6 |
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software | Name: RELION / Version: 3 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 891804 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164480 / Symmetry type: POINT |