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Yorodumi- EMDB-0937: Cryo-EM structure of the dithionite-reduced photosynthetic altern... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0937 | ||||||||||||||||||
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Title | Cryo-EM structure of the dithionite-reduced photosynthetic alternative complex III from Roseiflexus castenholzii | ||||||||||||||||||
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Sample |
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Function / homology | Function and homology information molybdopterin cofactor binding / electron transfer activity / oxidoreductase activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Shi Y / Xin YY / Wang C / Blankenship RE / Sun F / Xu XL | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: Sci Adv / Year: 2020 Title: Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from . Authors: Yang Shi / Yueyong Xin / Chao Wang / Robert E Blankenship / Fei Sun / Xiaoling Xu / Abstract: Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and ...Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and photosynthetic electron transport chains of bacteria. The coupling mechanism, however, is poorly understood. Here, we report the cryo-EM structures of air-oxidized and dithionite-reduced ACIII from the photosynthetic bacterium at 3.3- and 3.5-Å resolution, respectively. We identified a menaquinol binding pocket and an electron transfer wire comprising six hemes and four iron-sulfur clusters that is capable of transferring electrons to periplasmic acceptors. We detected a proton translocation passage in which three strictly conserved, mid-passage residues are likely essential for coupling the redox-driven proton translocation across the membrane. These results allow us to propose a previously unrecognized coupling mechanism that links the respiratory and photosynthetic functions of ACIII. This study provides a structural basis for further investigation of the energy transformation mechanisms in bacterial photosynthesis and respiration. | ||||||||||||||||||
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_0937.map.gz | 36 MB | EMDB map data format | |
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Header (meta data) | emd-0937-v30.xml emd-0937.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_0937.png | 166.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0937 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0937 | HTTPS FTP |
-Related structure data
Related structure data | 6loeMC 0936C 6lodC C: citing same article (ref.) M: atomic model generated by this map |
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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_0937.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 : Dithionite-reduced photosynthetic alternative complex III
+Supramolecule #1: Dithionite-reduced photosynthetic alternative complex III
+Macromolecule #1: MULTIHEME_CYTC domain-containing protein
+Macromolecule #2: Fe-S-cluster-containing hydrogenase components 1-like protein
+Macromolecule #3: Polysulphide reductase NrfD
+Macromolecule #4: Uncharacterized protein ActD
+Macromolecule #5: Cytochrome c domain-containing protein
+Macromolecule #6: Uncharacterized protein ActF
+Macromolecule #7: HEME C
+Macromolecule #8: IRON/SULFUR CLUSTER
+Macromolecule #9: FE3-S4 CLUSTER
+Macromolecule #10: [(2S)-2-octadecanoyloxypropyl] octadecanoate
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 488581 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 207633 |