+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32465 | ||||||||||||||||||
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Title | Subcomplexes A and E in NDH complex from Arabidopsis | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Subcomplex A / subcomplex E / supercomplex / Arabidopsis / plant / cyclic electron transport / ELECTRON TRANSPORT | ||||||||||||||||||
Function / homology | Function and homology information NAD(P)H dehydrogenase complex (plastoquinone) / NADH dehydrogenase complex (plastoquinone) assembly / cellular response to sulfate starvation / thylakoid membrane / chloroplast thylakoid / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADPH dehydrogenase activity / chloroplast envelope / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plastid ...NAD(P)H dehydrogenase complex (plastoquinone) / NADH dehydrogenase complex (plastoquinone) assembly / cellular response to sulfate starvation / thylakoid membrane / chloroplast thylakoid / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADPH dehydrogenase activity / chloroplast envelope / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plastid / chloroplast stroma / photosynthetic electron transport in photosystem I / photosynthesis, light reaction / chloroplast thylakoid membrane / NADH dehydrogenase (ubiquinone) activity / defense response to fungus / quinone binding / photosynthesis / chloroplast / NAD binding / 4 iron, 4 sulfur cluster binding / iron ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.33 Å | ||||||||||||||||||
Authors | Pan XW / Li M | ||||||||||||||||||
Funding support | China, 5 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_32465.map.gz | 226.6 MB | EMDB map data format | |
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Header (meta data) | emd-32465-v30.xml emd-32465.xml | 20 KB 20 KB | Display Display | EMDB header |
Images | emd_32465.png | 38.1 KB | ||
Filedesc metadata | emd-32465.cif.gz | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32465 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32465 | HTTPS FTP |
-Validation report
Summary document | emd_32465_validation.pdf.gz | 569 KB | Display | EMDB validaton report |
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Full document | emd_32465_full_validation.pdf.gz | 568.5 KB | Display | |
Data in XML | emd_32465_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_32465_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32465 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32465 | HTTPS FTP |
-Related structure data
Related structure data | 7wfgMC 7wfdC 7wfeC 7wffC 7wg5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32465.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
+Entire : Subcomplex A and E in NDH complex from Arabidopsis
+Supramolecule #1: Subcomplex A and E in NDH complex from Arabidopsis
+Macromolecule #1: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic
+Macromolecule #2: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
+Macromolecule #3: NAD(P)H-quinone oxidoreductase subunit J, chloroplastic
+Macromolecule #4: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
+Macromolecule #5: NAD(P)H-quinone oxidoreductase subunit L, chloroplastic
+Macromolecule #6: NAD(P)H-quinone oxidoreductase subunit M, chloroplastic
+Macromolecule #7: NAD(P)H-quinone oxidoreductase subunit N, chloroplastic
+Macromolecule #8: NdhO
+Macromolecule #9: NdhT
+Macromolecule #10: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76085 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |