+Open data
-Basic information
Entry | Database: PDB / ID: 7d6v | ||||||||||||
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Title | Mycobacterium smegmatis Sdh1 in complex with UQ1 | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / succinate dehydrogenase / electron transport chain / Mycobacterium smegmatis / Sdh1 / SQR | ||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors / tricarboxylic acid cycle / membrane => GO:0016020 / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å | ||||||||||||
Authors | Zhou, X. / Gao, Y. / Wang, Q. / Gong, H. / Rao, Z. | ||||||||||||
Funding support | China, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7d6v.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d6v.ent.gz | 165.7 KB | Display | PDB format |
PDBx/mmJSON format | 7d6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d6v_validation.pdf.gz | 1000.2 KB | Display | wwPDB validaton report |
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Full document | 7d6v_full_validation.pdf.gz | 1017 KB | Display | |
Data in XML | 7d6v_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 7d6v_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/7d6v ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d6v | HTTPS FTP |
-Related structure data
Related structure data | 30594MC 7d6xC 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 ... , 2 types, 2 molecules AC
#1: Protein | Mass: 70147.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) References: UniProt: A0A0D6G5S3, Oxidoreductases; Acting on the CH-CH group of donors |
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#3: Protein | Mass: 32583.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A0D6G6P6 |
-Protein , 1 types, 1 molecules B
#2: Protein | Mass: 28851.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A0D6G6K3 |
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-Non-polymers , 6 types, 7 molecules
#4: Chemical | ChemComp-FAD / | ||||||||
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#5: Chemical | #6: Chemical | ChemComp-SF4 / | #7: Chemical | ChemComp-F3S / | #8: Chemical | ChemComp-UQ1 / | #9: Chemical | ChemComp-PEV / ( | |
-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: Mycobacterium smegmatis Sdh1 in complex with UQ1 / Type: COMPLEX / Details: succinate dehydrogenase / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252092 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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