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Yorodumi- EMDB-10513: Structure of the NDH-1MS complex from Thermosynechococcus elongatus -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10513 | |||||||||||||||
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Title | Structure of the NDH-1MS complex from Thermosynechococcus elongatus | |||||||||||||||
Map data | Structure of the NDH-1MS complex from Thermosynechococcus elongatus | |||||||||||||||
Sample |
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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 / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / NAD binding / 4 iron, 4 sulfur cluster binding ...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 / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / iron ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) / Thermosynechococcus elongatus (strain BP-1) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
Authors | Schuller JM / Saura P / Thiemann J / Schuller SK / Gamiz-Hernandez AP / Kurisu G / Nowaczyk MM / Kaila VRI | |||||||||||||||
Funding support | Germany, 4 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I. Authors: Jan M Schuller / Patricia Saura / Jacqueline Thiemann / Sandra K Schuller / Ana P Gamiz-Hernandez / Genji Kurisu / Marc M Nowaczyk / Ville R I Kaila / Abstract: Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO) into organic molecules. Photorespiration, ...Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO) into organic molecules. Photorespiration, however, significantly reduces the photosynthetic yields. To survive under low CO concentrations, cyanobacteria evolved unique carbon-concentration mechanisms that enhance the efficiency of photosynthetic CO fixation, for which the molecular principles have remained unknown. We show here how modular adaptations enabled the cyanobacterial photosynthetic complex I to concentrate CO using a redox-driven proton-pumping machinery. Our cryo-electron microscopy structure at 3.2 Å resolution shows a catalytic carbonic anhydrase module that harbours a Zn active site, with connectivity to proton-pumping subunits that are activated by electron transfer from photosystem I. Our findings illustrate molecular principles in the photosynthetic complex I machinery that enabled cyanobacteria to survive in drastically changing CO conditions. | |||||||||||||||
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_10513.map.gz | 3.7 MB | EMDB map data format | |
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Header (meta data) | emd-10513-v30.xml emd-10513.xml | 33.3 KB 33.3 KB | Display Display | EMDB header |
Images | emd_10513.png | 128.1 KB | ||
Others | emd_10513_additional.map.gz | 50.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10513 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10513 | HTTPS FTP |
-Related structure data
Related structure data | 6tjvMC 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_10513.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the NDH-1MS complex from Thermosynechococcus elongatus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Structure of the NDH-1MS complex from Thermosynechococcus elongatus...
File | emd_10513_additional.map | ||||||||||||
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Annotation | Structure of the NDH-1MS complex from Thermosynechococcus elongatus (Local resolution filtered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : NDH-1MS
+Supramolecule #1: NDH-1MS
+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: NADH dehydrogenase subunit 4
+Macromolecule #5: NAD(P)H-quinone oxidoreductase subunit 4L
+Macromolecule #6: NADH dehydrogenase subunit 5
+Macromolecule #7: NADH dehydrogenase subunit 6
+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: Tlr0906 protein
+Macromolecule #17: Tll0220 protein
+Macromolecule #18: Tlr0636 protein
+Macromolecule #19: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #20: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #21: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #22: BETA-CAROTENE
+Macromolecule #23: CHLOROPHYLL A
+Macromolecule #24: IRON/SULFUR CLUSTER
+Macromolecule #25: ZINC ION
+Macromolecule #26: water
-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-PROPANE |
-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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170151 |