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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6929 | |||||||||
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Title | Cryo-EM structure of the red algal PSI-LHCR | |||||||||
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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 / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 76.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.7 KB 26.7 KB | Display Display | ![]() |
Images | ![]() | 75.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zgbMC ![]() 6930C ![]() 5zghC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : PSI-5Lhcr
+Supramolecule #1: PSI-5Lhcr
+Macromolecule #1: PsaA
+Macromolecule #2: PsaB
+Macromolecule #3: PsaC
+Macromolecule #4: PsaD
+Macromolecule #5: PsaE
+Macromolecule #6: PsaF
+Macromolecule #7: PsaI
+Macromolecule #8: PsaJ
+Macromolecule #9: PsaK
+Macromolecule #10: PsaL
+Macromolecule #11: PsaM
+Macromolecule #12: PsaO
+Macromolecule #13: Lhcr1
+Macromolecule #14: Lhcr2
+Macromolecule #15: Lhcr3
+Macromolecule #16: CHLOROPHYLL A ISOMER
+Macromolecule #17: CHLOROPHYLL A
+Macromolecule #18: PHYLLOQUINONE
+Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #20: BETA-CAROTENE
+Macromolecule #21: IRON/SULFUR CLUSTER
+Macromolecule #22: BETA-D-GLUCOSE
+Macromolecule #23: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #24: (2S)-2,3-dihydroxypropyl octadecanoate
+Macromolecule #25: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,...
+Macromolecule #26: 1-DODECANOL
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.0 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.17 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 124279 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |