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- EMDB-32477: Cyclic electron transport supercomplex NDH-PSI from Arabidopsis -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-32477 | ||||||||||||||||||
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Title | Cyclic electron transport supercomplex NDH-PSI from Arabidopsis | ||||||||||||||||||
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Function / homology | ![]() NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / photosystem I antenna complex / NADH dehydrogenase complex (plastoquinone) assembly / glucose-6-phosphate 1-epimerase activity / photosynthetic NADP+ reduction / photosystem I stabilization / cellular response to sulfate starvation / chloroplast photosystem I ...NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / photosystem I antenna complex / NADH dehydrogenase complex (plastoquinone) assembly / glucose-6-phosphate 1-epimerase activity / photosynthetic NADP+ reduction / photosystem I stabilization / cellular response to sulfate starvation / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / thylakoid lumen / pigment binding / chloroplast membrane / protein histidine kinase binding / response to high light intensity / P450-containing electron transport chain / thylakoid membrane / chloroplast thylakoid / plastoglobule / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem I reaction center / photosystem I / ubiquinone biosynthetic process / thylakoid / NADPH dehydrogenase activity / chloroplast envelope / photosystem I / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H / plastid / extrinsic component of membrane / chlorophyll binding / chloroplast stroma / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / NADH dehydrogenase activity / : / photosynthetic electron transport in photosystem I / mitochondrial electron transport, NADH to ubiquinone / chloroplast thylakoid membrane / mitochondrial respiratory chain complex I assembly / ubiquinone binding / response to light stimulus / NADH dehydrogenase (ubiquinone) activity / quinone binding / defense response to fungus / electron transport coupled proton transport / ATP synthesis coupled electron transport / photosynthesis / aerobic respiration / response to cold / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 2 iron, 2 sulfur cluster binding / NAD binding / protein folding / 4 iron, 4 sulfur cluster binding / carbohydrate binding / response to oxidative stress / membrane => GO:0016020 / carbohydrate metabolic process / oxidoreductase activity / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / calcium ion binding / magnesium ion binding / protein homodimerization activity / extracellular region / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 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 | ![]() | 227.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 61 KB 61 KB | Display Display | ![]() |
Images | ![]() | 109.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 533.4 KB | Display | ![]() |
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Full document | ![]() | 532.9 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wg5MC ![]() 7wfdC ![]() 7wfeC ![]() 7wffC ![]() 7wfgC 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 : Cyclic electron transfer supercomplex from Arabidopsis
+Supramolecule #1: Cyclic electron transfer supercomplex from 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 3-1, chloroplastic
+Macromolecule #15: Chlorophyll a-b binding protein 4, chloroplastic
+Macromolecule #16: Photosystem I chlorophyll a/b-binding protein 6, chloroplastic
+Macromolecule #17: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
+Macromolecule #18: Photosystem I chlorophyll a/b-binding protein 5, chloroplastic
+Macromolecule #19: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
+Macromolecule #20: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
+Macromolecule #21: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
+Macromolecule #22: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
+Macromolecule #23: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
+Macromolecule #24: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic
+Macromolecule #25: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
+Macromolecule #26: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic
+Macromolecule #27: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic
+Macromolecule #28: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic
+Macromolecule #29: NDH dependent flow 6
+Macromolecule #30: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic
+Macromolecule #31: Photosynthetic NDH subunit of lumenal location 1, chloroplastic
+Macromolecule #32: Photosynthetic NDH subunit of lumenal location 2, chloroplastic
+Macromolecule #33: Photosynthetic NDH subunit of lumenal location 3, chloroplastic
+Macromolecule #34: Photosynthetic NDH subunit of lumenal location 4, chloroplastic
+Macromolecule #35: Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, ch...
+Macromolecule #36: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic
+Macromolecule #37: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
+Macromolecule #38: NAD(P)H-quinone oxidoreductase subunit J, chloroplastic
+Macromolecule #39: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
+Macromolecule #40: NAD(P)H-quinone oxidoreductase subunit L, chloroplastic
+Macromolecule #41: NAD(P)H-quinone oxidoreductase subunit M, chloroplastic
+Macromolecule #42: NAD(P)H-quinone oxidoreductase subunit N, chloroplastic
+Macromolecule #43: NdhO
+Macromolecule #44: NdhT
+Macromolecule #45: CHLOROPHYLL A
+Macromolecule #46: PHYLLOQUINONE
+Macromolecule #47: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #48: BETA-CAROTENE
+Macromolecule #49: IRON/SULFUR CLUSTER
+Macromolecule #50: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #51: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #52: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #53: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #54: CHLOROPHYLL B
+Macromolecule #55: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #56: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #57: FE2/S2 (INORGANIC) CLUSTER
-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 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136022 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |