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Open data
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Basic information
Entry | Database: PDB / ID: 5zgb | ||||||
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Title | Cryo-EM structure of the red algal PSI-LHCR | ||||||
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![]() | PHOTOSYNTHESIS / super-complex / red alga / PSI-5Lhcr | ||||||
Function / homology | ![]() thylakoid membrane / 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 ...thylakoid membrane / 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 / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å | ||||||
![]() | Pi, X. | ||||||
![]() | ![]() Title: Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga. Authors: Xiong Pi / Lirong Tian / Huai-En Dai / Xiaochun Qin / Lingpeng Cheng / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen / ![]() ![]() Abstract: Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic ...Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 758.8 KB | Display | ![]() |
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PDB format | ![]() | 684 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 11.1 MB | Display | ![]() |
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Full document | ![]() | 11.6 MB | Display | |
Data in XML | ![]() | 207.1 KB | Display | |
Data in CIF | ![]() | 250 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6929MC ![]() 6930C ![]() 5zghC 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 , 12 types, 14 molecules ABCDEFKLO14253
#1: Protein | Mass: 82763.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FY7, photosystem I | ||||
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#2: Protein | Mass: 82107.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FY6, photosystem I | ||||
#3: Protein | Mass: 8822.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85G47, photosystem I | ||||
#4: Protein | Mass: 15698.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FY0 | ||||
#5: Protein | Mass: 10545.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FZ1 | ||||
#6: Protein | Mass: 21239.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FS9 | ||||
#9: Protein | Mass: 6295.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85G51 | ||||
#10: Protein | Mass: 15157.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FP8 | ||||
#12: Protein | Mass: 16744.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: M1VFJ4 | ||||
#13: Protein | Mass: 19808.818 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: M1VKK5 #14: Protein | Mass: 21960.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: M1UU36 #15: Protein | | Mass: 20458.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D |
-Protein/peptide , 3 types, 3 molecules IJM
#7: Protein/peptide | Mass: 3408.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FQ6 |
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#8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85FS8 |
#11: Protein/peptide | Mass: 3139.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 10D / References: UniProt: Q85G73 |
-Sugars , 2 types, 2 molecules ![](data/chem/img/BGC.gif)
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![](data/chem/img/DGD.gif)
#22: Sugar | ChemComp-BGC / |
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#23: Sugar | ChemComp-DGD / |
-Non-polymers , 9 types, 213 molecules ![](data/chem/img/CL0.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/3XQ.gif)
![](data/chem/img/ZEX.gif)
![](data/chem/img/1DO.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/3XQ.gif)
![](data/chem/img/ZEX.gif)
![](data/chem/img/1DO.gif)
#16: Chemical | ChemComp-CL0 / | ||||||||||||||
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#17: Chemical | ChemComp-CLA / #18: Chemical | #19: Chemical | #20: Chemical | ChemComp-BCR / #21: Chemical | #24: Chemical | ChemComp-3XQ / ( | #25: Chemical | ChemComp-ZEX / ( #26: Chemical | ChemComp-1DO / | |
-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-5Lhcr / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN / Humidity: 100 % |
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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: 2.17 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Version: 1.4 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124279 / Symmetry type: POINT | ||||||||||||||||||||||||
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