+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0849 | |||||||||
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Title | cryo-EM structure of cyanobacteria Fd-NDH-1L complex | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | photosystem I / cyclic electron transfer / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information : / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity ...: / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Zhang C / Shuai J | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural insights into NDH-1 mediated cyclic electron transfer. Authors: Chunli Zhang / Jin Shuai / Zhaoxing Ran / Jiaohong Zhao / Zhenfang Wu / Rijing Liao / Jian Wu / Weimin Ma / Ming Lei / Abstract: NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution ...NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus. The structure reveals three β-carotene and fifteen lipid molecules in the membrane arm of NDH-1L. Regulatory oxygenic photosynthesis-specific (OPS) subunits NdhV, NdhS and NdhO are close to the Fd-binding site whilst NdhL is adjacent to the plastoquinone (PQ) cavity, and they play different roles in PSI CET under high-light stress. NdhV assists in the binding of Fd to NDH-1L and accelerates PSI CET in response to short-term high-light exposure. In contrast, prolonged high-light irradiation switches on the expression and assembly of the NDH-1MS complex, which likely contains no NdhO to further accelerate PSI CET and reduce ROS production. We propose that this hierarchical mechanism is necessary for the survival of cyanobacteria in an aerobic environment. | |||||||||
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_0849.map.gz | 96 MB | EMDB map data format | |
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Header (meta data) | emd-0849-v30.xml emd-0849.xml | 33.6 KB 33.6 KB | Display Display | EMDB header |
Images | emd_0849.png | 135.9 KB | ||
Filedesc metadata | emd-0849.cif.gz | 9.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0849 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0849 | HTTPS FTP |
-Validation report
Summary document | emd_0849_validation.pdf.gz | 588.9 KB | Display | EMDB validaton report |
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Full document | emd_0849_full_validation.pdf.gz | 588.4 KB | Display | |
Data in XML | emd_0849_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_0849_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0849 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0849 | HTTPS FTP |
-Related structure data
Related structure data | 6l7oMC 0850C 0851C 6l7pC 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_0849.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 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 : Fd-NDH-1L complex
+Supramolecule #1: Fd-NDH-1L complex
+Macromolecule #1: NAD(P)H-quinone oxidoreductase subunit 1
+Macromolecule #2: NAD(P)H-quinone oxidoreductase subunit 2
+Macromolecule #3: NAD(P)H-quinone oxidoreductase subunit 3
+Macromolecule #4: NAD(P)H-quinone oxidoreductase chain 4 1
+Macromolecule #5: NAD(P)H-quinone oxidoreductase subunit 4L
+Macromolecule #6: NADH dehydrogenase subunit 5
+Macromolecule #7: NADH-quinone oxidoreductase subunit J
+Macromolecule #8: NAD(P)H-quinone oxidoreductase subunit H
+Macromolecule #9: NAD(P)H-quinone oxidoreductase subunit I
+Macromolecule #10: NAD(P)H-quinone oxidoreductase subunit J
+Macromolecule #11: NAD(P)H-quinone oxidoreductase subunit K
+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: NAD(P)H-quinone oxidoreductase subunit O
+Macromolecule #16: NAD(P)H-quinone oxidoreductase subunit P
+Macromolecule #17: NAD(P)H-quinone oxidoreductase subunit Q
+Macromolecule #18: Ferredoxin-1
+Macromolecule #19: Tlr0636 protein
+Macromolecule #20: Tlr0472 protein
+Macromolecule #21: BETA-CAROTENE
+Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #23: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #24: Digitonin
+Macromolecule #25: PHYLLOQUINONE
+Macromolecule #26: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #27: IRON/SULFUR CLUSTER
+Macromolecule #28: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338822 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |