+Open data
-Basic information
Entry | Database: PDB / ID: 6lum | ||||||||||||
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Title | Structure of Mycobacterium smegmatis succinate dehydrogenase 2 | ||||||||||||
Components | (Succinate dehydrogenase subunit ...) x 5 | ||||||||||||
Keywords | OXIDOREDUCTASE / electron transfer chain / trimer | ||||||||||||
Function / homology | Function and homology information succinate dehydrogenase / : / succinate dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / electron transport chain / flavin adenine dinucleotide binding ...succinate dehydrogenase / : / succinate dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / electron transport chain / flavin adenine dinucleotide binding / membrane => GO:0016020 / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mycolicibacterium smegmatis MC2 51 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||
Authors | Gao, Y. / Gong, H. / Zhou, X. / Xiao, Y. / Wang, W. / Ji, W. / Wang, Q. / Rao, Z. | ||||||||||||
Funding support | China, 3items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lum.cif.gz | 597.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lum.ent.gz | 480.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lum_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6lum_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6lum_validation.xml.gz | 119.1 KB | Display | |
Data in CIF | 6lum_validation.cif.gz | 162.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6lum ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6lum | HTTPS FTP |
-Related structure data
Related structure data | 0981MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Succinate dehydrogenase subunit ... , 5 types, 15 molecules CGMDHNEIOAJPBKQ
#1: Protein | Mass: 15644.627 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria) Strain: MC2 51 / References: UniProt: A0QT10*PLUS #2: Protein | Mass: 19280.400 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria) Strain: MC2 51 / References: UniProt: A0QT09*PLUS #3: Protein/peptide | Mass: 3707.443 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria) Strain: MC2 51 / References: UniProt: A0R4D1*PLUS #4: Protein | Mass: 64476.754 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria) Strain: MC2 51 / References: UniProt: A0QT08*PLUS #5: Protein | Mass: 29245.760 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria) Strain: MC2 51 / References: UniProt: A0QT07*PLUS |
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-Non-polymers , 10 types, 39 molecules
#6: Chemical | ChemComp-PEV / ( #7: Chemical | ChemComp-HEM / #8: Chemical | ChemComp-MQ9 / #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | #13: Chemical | #14: Chemical | #15: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mycobaterium smegmatis Succinate dehydrogenase 2 / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.4 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: mc2 51 | ||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: Solutions were made fresh | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono disperse. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Average exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 461385 / Algorithm: FOURIER SPACE Details: cryoSPARC software was used for the reconstruction. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Highest resolution: 2.84 Å | ||||||||||||||||||||||||||||
Refine LS restraints |
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