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- EMDB-38012: Cryo-EM structure of the photosynthetic alternative complex III w... -
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Open data
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Basic information
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Title | Cryo-EM structure of the photosynthetic alternative complex III with a quinone inhibitor HQNO from Chloroflexus aurantiacus | |||||||||
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![]() | Photosynthetic alternative complex III / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Xu X | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of HQNO-bound Alternative Complex III from the anoxygenic phototrophic bacterium Chloroflexus aurantiacus. Authors: Jiyu Xin / Zhenzhen Min / Lu Yu / Xinyi Yuan / Aokun Liu / Wenping Wu / Xin Zhang / Huimin He / Jingyi Wu / Yueyong Xin / Robert E Blankenship / Changlin Tian / Xiaoling Xu / ![]() ![]() Abstract: Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the ...Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the cytochrome bc1/b6f complexes, but functionally replaces these enzymes in the photosynthetic and/or respiratory electron transport chains (ETCs) of many bacteria. However, the true compositions and architectures of ACIIIs remain unclear, as do their structural and functional relevance in mediating the ETCs. We here determined cryogenic electron microscopy structures of photosynthetic ACIII isolated from Chloroflexus aurantiacus (CaACIIIp), in apo-form and in complexed form bound to a menadiol analog 2-heptyl-4-hydroxyquinoline-N-oxide (HQNO). Besides six canonical subunits (ActABCDEF), the structures revealed conformations of two previously unresolved subunits, ActG and I, which contributed to the complex stability. We also elucidated the structural basis of menaquinol oxidation and subsequent electron transfer along the [3Fe-4S]-6 hemes wire to its periplasmic electron acceptors, using electron paramagnetic resonance (EPR), spectroelectrochemistry, enzymatic analyses and molecular dynamics (MD) simulations. A unique insertion loop in ActE was shown to function in determining the binding specificity of CaACIIIp for downstream electron acceptors. This study broadens our understanding of the structural diversity and molecular evolution of ACIIIs, enabling further investigation of the (mena)quinol oxidoreductases evolved coupling mechanism in bacterial energy conservation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 36.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.8 KB 24.8 KB | Display Display | ![]() |
Images | ![]() | 148.4 KB | ||
Filedesc metadata | ![]() | 7.8 KB | ||
Others | ![]() ![]() | 35.7 MB 35.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8x2jMC ![]() 8k9eC ![]() 8k9fC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38012_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38012_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Alternative complex III
+Supramolecule #1: Alternative complex III
+Macromolecule #1: Cytochrome c7-like domain-containing protein
+Macromolecule #2: Fe-S-cluster-containing hydrogenase components 1-like protein
+Macromolecule #3: Polysulphide reductase NrfD
+Macromolecule #4: Quinol:cytochrome c oxidoreductase membrane protein
+Macromolecule #5: Cytochrome c domain-containing protein
+Macromolecule #6: Quinol:cytochrome c oxidoreductase quinone-binding subunit 2
+Macromolecule #7: Uncharacterized protein
+Macromolecule #8: unknown
+Macromolecule #9: HEME C
+Macromolecule #10: IRON/SULFUR CLUSTER
+Macromolecule #11: FE3-S4 CLUSTER
+Macromolecule #12: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoy...
+Macromolecule #13: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
+Macromolecule #14: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoy...
+Macromolecule #15: 1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160264 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |