+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30594 | ||||||||||||
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Title | Mycobacterium smegmatis Sdh1 in complex with UQ1 | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Mycolicibacterium smegmatis MC2 51 (bacteria) / Mycolicibacterium smegmatis (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.53 Å | ||||||||||||
Authors | Zhou X / Gao Y / Wang Q / Gong H / Rao Z | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster. Authors: Xiaoting Zhou / Yan Gao / Weiwei Wang / Xiaolin Yang / Xiuna Yang / Fengjiang Liu / Yanting Tang / Sin Man Lam / Guanghou Shui / Lu Yu / Changlin Tian / Luke W Guddat / Quan Wang / Zihe Rao / Hongri Gong / Abstract: Complex II, also known as succinate dehydrogenase (SQR) or fumarate reductase (QFR), is an enzyme involved in both the Krebs cycle and oxidative phosphorylation. Mycobacterial Sdh1 has recently been ...Complex II, also known as succinate dehydrogenase (SQR) or fumarate reductase (QFR), is an enzyme involved in both the Krebs cycle and oxidative phosphorylation. Mycobacterial Sdh1 has recently been identified as a new class of respiratory complex II (type F) but with an unknown electron transfer mechanism. Here, using cryoelectron microscopy, we have determined the structure of Sdh1 in the presence and absence of the substrate, ubiquinone-1, at 2.53-Å and 2.88-Å resolution, respectively. Sdh1 comprises three subunits, two that are water soluble, SdhA and SdhB, and one that is membrane spanning, SdhC. Within these subunits we identified a quinone-binding site and a rarely observed Rieske-type [2Fe-2S] cluster, the latter being embedded in the transmembrane region. A mutant, where two His ligands of the Rieske-type [2Fe-2S] were changed to alanine, abolished the quinone reduction activity of the Sdh1. Our structures allow the proposal of an electron transfer pathway that connects the substrate-binding and quinone-binding sites. Given the unique features of Sdh1 and its essential role in , these structures will facilitate antituberculosis drug discovery efforts that specifically target this complex. | ||||||||||||
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_30594.map.gz | 204 MB | EMDB map data format | |
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Header (meta data) | emd-30594-v30.xml emd-30594.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_30594.png | 113.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30594 | HTTPS FTP |
-Related structure data
Related structure data | 7d6vMC 7d6xC 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_30594.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 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 : Mycobacterium smegmatis Sdh1 in complex with UQ1
+Supramolecule #1: Mycobacterium smegmatis Sdh1 in complex with UQ1
+Macromolecule #1: Succinate dehydrogenase subunit A
+Macromolecule #2: Fumarate reductase iron-sulfur subunit
+Macromolecule #3: Succinate dehydrogenase (Membrane anchor subunit)
+Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE
+Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #6: IRON/SULFUR CLUSTER
+Macromolecule #7: FE3-S4 CLUSTER
+Macromolecule #8: UBIQUINONE-1
+Macromolecule #9: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II |
-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 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 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: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 252092 |