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Open data
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Basic information
Entry | Database: PDB / ID: 6igz | ||||||
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Title | Structure of PSI-LHCI | ||||||
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![]() | PLANT PROTEIN / PSI-LHCI | ||||||
Function / homology | ![]() photosynthesis, light harvesting / thylakoid membrane / : / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...photosynthesis, light harvesting / thylakoid membrane / : / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å | ||||||
![]() | Xiong, P. / Xiaochun, Q. | ||||||
![]() | ![]() Title: Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits. Authors: Xiaochun Qin / Xiong Pi / Wenda Wang / Guangye Han / Lixia Zhu / Mingmei Liu / Linpeng Cheng / Jian-Ren Shen / Tingyun Kuang / Sen-Fang Sui / ![]() ![]() Abstract: Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an ...Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an extremely large light-harvesting complex I (LHCI) captures and transfers energy to the PSI core. Here, we report the structure of PSI-LHCI from a green alga Bryopsis corticulans at 3.49 Å resolution, obtained by single-particle cryo-electron microscopy, which revealed 13 core subunits including subunits characteristic of both prokaryotes and eukaryotes, and 10 light-harvesting complex a (Lhca) antennas that form a double semi-ring and an additional Lhca dimer, including a novel four-transmembrane-helix Lhca. In total, 244 chlorophylls were identified, some of which were located at key positions for the fast energy transfer. These results provide a firm structural basis for unravelling the mechanisms of light-energy harvesting, transfer and quenching in the green algal PSI-LHCI, and important clues as to how PSI-LHCI has changed during evolution. | ||||||
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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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 15.4 MB | Display | ![]() |
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Full document | ![]() | 16.7 MB | Display | |
Data in XML | ![]() | 324 KB | Display | |
Data in CIF | ![]() | 377.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9670MC 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 , 18 types, 20 molecules ABCDEFGHKL1523486790
#1: Protein | Mass: 83412.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
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#2: Protein | Mass: 82164.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#3: Protein | Mass: 8880.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#4: Protein | Mass: 21733.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#5: Protein | Mass: 10096.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#6: Protein | Mass: 25129.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#7: Protein | Mass: 18226.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#8: Protein | Mass: 14400.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#11: Protein | Mass: 12487.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#12: Protein | Mass: 21338.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||
#13: Protein | Mass: 24458.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | | Mass: 27808.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | | Mass: 30409.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | Mass: 26575.912 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | | Mass: 29300.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | | Mass: 28621.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | | Mass: 24152.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein | | Mass: 26910.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 3 types, 3 molecules IJM
#9: Protein/peptide | Mass: 3859.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#10: Protein/peptide | Mass: 4744.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein/peptide | Mass: 3505.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 2 types, 3 molecules ![](data/chem/img/HTG.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#26: Sugar | #28: Sugar | ChemComp-DGD / | |
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-Non-polymers , 8 types, 317 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/8CT.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/8CT.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/CHL.gif)
![](data/chem/img/XAT.gif)
![](data/chem/img/LMG.gif)
#22: Chemical | ChemComp-CLA / #23: Chemical | #24: Chemical | ChemComp-LHG / #25: Chemical | ChemComp-8CT / ( #27: Chemical | #29: Chemical | ChemComp-CHL / #30: Chemical | ChemComp-XAT / ( #31: Chemical | |
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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: PSI-LHCI / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 3 mg/ml / 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: 1.852 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Version: 1.4 / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59525 / Symmetry type: POINT | ||||||||||||||||||||||||
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