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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31348 | |||||||||
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Title | Barley photosystem I-LHCI-Lhca5 supercomplex | |||||||||
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Function / homology | ![]() photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I ...photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Wang WD / Shen L / Tang K / Han GY / Zhang X / Shen JR | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare. Authors: Liangliang Shen / Kailu Tang / Wenda Wang / Chen Wang / Hangjun Wu / Zhiyuan Mao / Shaoya An / Shenghai Chang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Xing Zhang / ![]() ![]() Abstract: The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex ...The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET. #1: ![]() Title: Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex Authors: Qin XC / Suga M / Kuang TY / Shen JR | |||||||||
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 | ![]() | 307 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.4 KB 29.4 KB | Display Display | ![]() |
Images | ![]() | 59.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ew6MC ![]() 7eu3C ![]() 7ewkC ![]() 7f9oC 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: 1.307 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-LHCI-Lhca5 supercomplex of Barley
+Supramolecule #1: PSI-LHCI-Lhca5 supercomplex of Barley
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #3: Photosystem I iron-sulfur center
+Macromolecule #4: Photosystem I reaction center subunit II, chloroplastic
+Macromolecule #5: Photosystem I reaction center subunit IV, chloroplastic
+Macromolecule #6: Photosystem I reaction center subunit III, chloroplastic
+Macromolecule #7: Photosystem I reaction center subunit VI, chloroplastic
+Macromolecule #8: Photosystem I reaction center subunit VIII
+Macromolecule #9: Photosystem I reaction center subunit IX
+Macromolecule #10: Photosystem I reaction center subunit psaK, chloroplastic
+Macromolecule #11: Photosystem I reaction center subunit XI, chloroplastic
+Macromolecule #12: Chlorophyll a-b binding protein Lhca1
+Macromolecule #13: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #15: Chlorophyll a-b binding protein Lhca5
+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: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #23: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #24: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #25: CHLOROPHYLL B
+Macromolecule #26: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103844 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |