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- PDB-8j5k: Structural insights into photosystem II supercomplex and trimeric... -
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Basic information
Entry | Database: PDB / ID: 8j5k | ||||||
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Title | Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana | ||||||
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![]() | PHOTOSYNTHESIS / PSII-FCPII supercomplex | ||||||
Function / homology | ![]() Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-ET4 / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD Similarity search - Component | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||
![]() | Shen, L.L. / Li, Z.H. / Shen, J.R. / Wang, W.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana. Authors: Songhao Zhao / Lili Shen / Xiaoyi Li / Qiushuang Tao / Zhenhua Li / Caizhe Xu / Cuicui Zhou / Yanyan Yang / Min Sang / Guangye Han / Long-Jiang Yu / Tingyun Kuang / Jian-Ren Shen / Wenda Wang / ![]() ![]() Abstract: Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific ...Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 16.7 MB | Display | ![]() |
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Full document | ![]() | 17.3 MB | Display | |
Data in XML | ![]() | 323.7 KB | Display | |
Data in CIF | ![]() | 411.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35987MC ![]() 8j7zC ![]() 8w4oC ![]() 8w4pC 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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Assembly
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Components
-Protein , 17 types, 34 molecules AaBbCcDdEeHhOoQqUuVvZz507261pP...
#1: Protein | Mass: 36951.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 53504.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 49357.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 37826.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 8687.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 7188.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 26749.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 16001.864 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | Mass: 10010.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | Mass: 14757.663 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #22: Protein | Mass: 6233.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #23: Protein | Mass: 18512.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #24: Protein | Mass: 18251.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #25: Protein | Mass: 18085.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #26: Protein | Mass: 23279.170 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Protein | Mass: 13039.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #28: Protein | Mass: 17850.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein/peptide , 11 types, 22 molecules FfIiJjKkLlMmNnTtWwXxYy
#6: Protein/peptide | Mass: 3555.263 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein/peptide | Mass: 3940.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein/peptide | Mass: 3487.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein/peptide | Mass: 4225.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein/peptide | Mass: 4235.880 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein/peptide | Mass: 4358.022 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein/peptide | Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein/peptide | Mass: 3441.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein/peptide | Mass: 5606.405 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein/peptide | Mass: 3389.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #21: Protein/peptide | Mass: 3634.343 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 1 types, 8 molecules ![](data/chem/img/DGD.gif)
#39: Sugar | ChemComp-DGD / |
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-Non-polymers , 15 types, 328 molecules ![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/ET4.gif)
![](data/chem/img/DD6.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/ET4.gif)
![](data/chem/img/DD6.gif)
#29: Chemical | #30: Chemical | #31: Chemical | ChemComp-CLA / #32: Chemical | ChemComp-PHO / #33: Chemical | ChemComp-BCR / #34: Chemical | ChemComp-SQD / #35: Chemical | ChemComp-PL9 / #36: Chemical | ChemComp-LHG / #37: Chemical | ChemComp-LMG / #38: Chemical | #40: Chemical | #41: Chemical | ChemComp-HEM / #42: Chemical | ChemComp-A86 / ( #43: Chemical | |
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