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- EMDB-32463: Right PSI in the cyclic electron transfer supercomplex NDH-PSI fr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-32463 | ||||||||||||||||||
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Title | Right PSI in the cyclic electron transfer supercomplex NDH-PSI from Arabidopsis | ||||||||||||||||||
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Function / homology | ![]() photosystem I antenna complex / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / pigment binding / chloroplast membrane / response to high light intensity / chloroplast thylakoid ...photosystem I antenna complex / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / pigment binding / chloroplast membrane / response to high light intensity / chloroplast thylakoid / plastoglobule / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / protein homodimerization activity / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | ||||||||||||||||||
![]() | Pan XW / Li M | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana. Authors: Xiaodong Su / Duanfang Cao / Xiaowei Pan / Lifang Shi / Zhenfeng Liu / Luca Dall'Osto / Roberto Bassi / Xinzheng Zhang / Mei Li / ![]() ![]() Abstract: Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane- ...Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants. | ||||||||||||||||||
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 | ![]() | 226.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.9 KB 29.9 KB | Display Display | ![]() |
Images | ![]() | 50.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wfeMC ![]() 7wfdC ![]() 7wffC ![]() 7wfgC ![]() 7wg5C 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: 1.04 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 complex in the NDH-PSI supercomplex of Arabidopsis
+Supramolecule #1: PSI complex in the NDH-PSI supercomplex of Arabidopsis
+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-2, chloroplastic
+Macromolecule #5: Photosystem I reaction center subunit IV A, chloroplastic
+Macromolecule #6: Photosystem I reaction center subunit III, chloroplastic
+Macromolecule #7: Photosystem I reaction center subunit V, chloroplastic
+Macromolecule #8: Photosystem I reaction center subunit VI-2, chloroplastic
+Macromolecule #9: Photosystem I reaction center subunit VIII
+Macromolecule #10: Photosystem I reaction center subunit IX
+Macromolecule #11: Photosystem I reaction center subunit psaK, chloroplastic
+Macromolecule #12: Photosystem I reaction center subunit XI, chloroplastic
+Macromolecule #13: Chlorophyll a-b binding protein 6, chloroplastic
+Macromolecule #14: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
+Macromolecule #15: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
+Macromolecule #16: Photosystem I chlorophyll a/b-binding protein 5, chloroplastic
+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: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #23: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #24: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #25: CHLOROPHYLL B
+Macromolecule #26: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #27: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
-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: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
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 | Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136022 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |