National Natural Science Foundation of China (NSFC)
81520108019, 813300237
China
Chinese Academy of Sciences
2017YFC0840300
China
Citation
Journal: Nat Commun / Year: 2020 Title: Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF. Authors: Hongri Gong / Yan Gao / Xiaoting Zhou / Yu Xiao / Weiwei Wang / Yanting Tang / Shan Zhou / Yuying Zhang / Wenxin Ji / Lu Yu / Changlin Tian / Sin Man Lam / Guanghou Shui / Luke W Guddat / ...Authors: Hongri Gong / Yan Gao / Xiaoting Zhou / Yu Xiao / Weiwei Wang / Yanting Tang / Shan Zhou / Yuying Zhang / Wenxin Ji / Lu Yu / Changlin Tian / Sin Man Lam / Guanghou Shui / Luke W Guddat / Luet-Lok Wong / Quan Wang / Zihe Rao / Abstract: Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by ...Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.
History
Deposition
Jan 29, 2020
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Header (metadata) release
May 27, 2020
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Map release
May 27, 2020
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Update
May 29, 2024
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Current status
May 29, 2024
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II
Details
This sample was mono disperse.
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Startup model
Type of model: EMDB MAP
Final reconstruction
Number classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC Details: cryoSPARC software was used for the reconstruction. Number images used: 461385
Initial angle assignment
Type: COMMON LINE / Software - Name: cryoSPARC
Final angle assignment
Type: COMMON LINE / Software - Name: cryoSPARC
Final 3D classification
Software - Name: cryoSPARC
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