+Open data
-Basic information
Entry | Database: PDB / ID: 7wg5 | ||||||||||||||||||
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Title | Cyclic electron transport supercomplex NDH-PSI from Arabidopsis | ||||||||||||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Supercomplex / PSI / NDH-PSI / plant / Arabidopsis / cyclic electron transport | ||||||||||||||||||
Function / homology | Function and homology information 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 / ubiquinone biosynthetic process / chloroplast thylakoid lumen / photosystem II oxygen evolving complex / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / 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 / NADH dehydrogenase activity / plastid / chloroplast stroma / extrinsic component of membrane / chlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem I / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / chloroplast thylakoid membrane / 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 / 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 / electron transfer activity / oxidoreductase 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å | ||||||||||||||||||
Authors | Pan, X.W. / Li, M. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Mol Plant / Year: 2022 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7wg5.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7wg5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7wg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wg5 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wg5 | HTTPS FTP |
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-Related structure data
Related structure data | 32477MC 7wfdC 7wfeC 7wffC 7wfgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 4 molecules AABAABBB
+Protein , 6 types, 7 molecules ACBCDdjOT
+Photosystem I reaction center subunit ... , 9 types, 18 molecules ADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBL
+Chlorophyll a-b binding protein ... , 2 types, 3 molecules A1B1A4
+Photosystem I chlorophyll a/b-binding protein ... , 4 types, 5 molecules A3B3A6B2B5
+NAD(P)H-quinone oxidoreductase subunit ... , 13 types, 13 molecules ABCEFGHIJKLMN
+Photosynthetic NDH subunit of subcomplex B ... , 4 types, 4 molecules abce
+Photosynthetic NDH subunit of lumenal location ... , 4 types, 4 molecules fghi
+Sugars , 2 types, 10 molecules
+Non-polymers , 11 types, 413 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cyclic electron transfer supercomplex from Arabidopsis Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136022 / Symmetry type: POINT |