+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31307 | |||||||||
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Title | Chloroplast NDH complex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / chloroplast thylakoid membrane / photosynthesis, light reaction / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / mitochondrial membrane / NAD binding / 4 iron, 4 sulfur cluster binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / chloroplast thylakoid membrane / photosynthesis, light reaction / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / mitochondrial membrane / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / iron ion binding Similarity search - Function | |||||||||
Biological species | Hordeum vulgare subsp. spontaneum (wild barley) / Hordeum vulgare (barley) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Wang WD / Shen L / Tang K / Han GY / Zhang X / Shen JR | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2022 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. | |||||||||
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_31307.map.gz | 304.6 MB | EMDB map data format | |
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Header (meta data) | emd-31307-v30.xml emd-31307.xml | 36.7 KB 36.7 KB | Display Display | EMDB header |
Images | emd_31307.png | 46.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31307 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31307 | HTTPS FTP |
-Related structure data
Related structure data | 7eu3MC 7ew6C 7ewkC 7f9oC 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_31307.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
+Entire : Chloroplast NDH complex of Barley
+Supramolecule #1: Chloroplast NDH complex of Barley
+Macromolecule #1: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
+Macromolecule #2: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
+Macromolecule #3: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
+Macromolecule #4: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
+Macromolecule #5: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
+Macromolecule #6: NAD(P)H-quinone oxidoreductase subunit F
+Macromolecule #7: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
+Macromolecule #8: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic
+Macromolecule #9: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
+Macromolecule #10: NAD(P)H-quinone oxidoreductase subunit J
+Macromolecule #11: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
+Macromolecule #12: NAD(P)H-quinone oxidoreductase subunit L
+Macromolecule #13: NAD(P)H-quinone oxidoreductase subunit M
+Macromolecule #14: NAD(P)H-quinone oxidoreductase subunit N
+Macromolecule #15: Unidentified stromal protein
+Macromolecule #16: Photosynthetic NDH subunit of subcomplex L1
+Macromolecule #17: Photosynthetic NDH subunit of subcomplex L2
+Macromolecule #18: Photosynthetic NDH subunit of subcomplex L3
+Macromolecule #19: Photosynthetic NDH subunit of subcomplex L4
+Macromolecule #20: Photosynthetic NDH subunit of subcomplex L5
+Macromolecule #21: Photosynthetic NDH subunit of subcomplex B1
+Macromolecule #22: Photosynthetic NDH subunit of subcomplex B2
+Macromolecule #23: Photosynthetic NDH subunit of subcomplex B3
+Macromolecule #24: Photosynthetic NDH subunit of subcomplex B4
+Macromolecule #25: Photosynthetic NDH subunit of subcomplex B5
+Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #27: BETA-CAROTENE
+Macromolecule #28: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #29: 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: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103844 |