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Yorodumi- PDB-9fu0: CIII2/CIV respiratory chain supercomplex from Mycobacterium smegmatis -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9fu0 | ||||||
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| Title | CIII2/CIV respiratory chain supercomplex from Mycobacterium smegmatis | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / RESPIRATORY SUPERCOMPLEX / MEMBRANE PROTEIN / ACTINOBACTERIA | ||||||
| Function / homology | Function and homology informationaerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ...aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ATP synthesis coupled electron transport / respiratory electron transport chain / monooxygenase activity / electron transport chain / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / heme binding / metal ion binding / membrane / plasma membrane Similarity search - Function | ||||||
| Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Kovalova, T. / Krol, S. / Gamiz-Hernandez, A. / Sjostrand, D. / Kaila, V. / Brzezinski, P. / Hogbom, M. | ||||||
| Funding support | Sweden, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024Title: Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide. Authors: Terezia Kovalova / Sylwia Król / Ana P Gamiz-Hernandez / Dan Sjöstrand / Ville R I Kaila / Peter Brzezinski / Martin Högbom / ![]() Abstract: Tuberculosis is one of the most common causes of death worldwide, with a rapid emergence of multi-drug-resistant strains underscoring the need for new antituberculosis drugs. Recent studies indicate ...Tuberculosis is one of the most common causes of death worldwide, with a rapid emergence of multi-drug-resistant strains underscoring the need for new antituberculosis drugs. Recent studies indicate that lansoprazole-a known gastric proton pump inhibitor and its intracellular metabolite, lansoprazole sulfide (LPZS)-are potential antituberculosis compounds. Yet, their inhibitory mechanism and site of action still remain unknown. Here, we combine biochemical, computational, and structural approaches to probe the interaction of LPZS with the respiratory chain supercomplex IIIIV of , a close homolog of supercomplex. We show that LPZS binds to the Q cavity of the mycobacterial supercomplex, inhibiting the quinol substrate oxidation process and the activity of the enzyme. We solve high-resolution (2.6 Å) cryo-electron microscopy (cryo-EM) structures of the supercomplex with bound LPZS that together with microsecond molecular dynamics simulations, directed mutagenesis, and functional assays reveal key interactions that stabilize the inhibitor, but also how mutations can lead to the emergence of drug resistance. Our combined findings reveal an inhibitory mechanism of LPZS and provide a structural basis for drug development against tuberculosis. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9fu0.cif.gz | 724.7 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9fu0.ent.gz | 568.9 KB | Display | PDB format |
| PDBx/mmJSON format | 9fu0.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9fu0_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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| Full document | 9fu0_full_validation.pdf.gz | 4 MB | Display | |
| Data in XML | 9fu0_validation.xml.gz | 141.7 KB | Display | |
| Data in CIF | 9fu0_validation.cif.gz | 188.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/9fu0 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/9fu0 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 50753MC ![]() 9ftzC C: citing same article ( M: map data used to model this data |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Assembly
| Deposited unit | ![]()
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.99220961754, -0.108820525247, -0.0606479030678), (-0.10999524735, -0.993797299749, -0.0163698678167), (-0.0584903446902, 0.0229133213847, -0.998024979287)Vector: 12. ...NCS oper: (Code: given Matrix: (0.99220961754, -0.108820525247, -0.0606479030678), Vector: |
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Components
-Cytochrome bc1 complex cytochrome c ... , 2 types, 3 molecules OMG
| #1: Protein | Mass: 29109.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4261 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R050, quinol-cytochrome-c reductase |
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| #2: Protein | Mass: 44869.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4261 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R051, quinol-cytochrome-c reductase |
-Protein , 7 types, 9 molecules NHPSQVWYc
| #3: Protein | Mass: 61514.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4263 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R052, quinol-cytochrome-c reductase#4: Protein | | Mass: 11329.909 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_2575 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QVH4#5: Protein | | Mass: 22196.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4260 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R049#8: Protein | | Mass: 38077.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4268 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R057, cytochrome-c oxidase#10: Protein | | Mass: 15910.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4692, MSMEI_4575 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R1B5#11: Protein | | Mass: 19118.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_6078 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R562#12: Protein | Mass: 23232.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: sodC, MSMEG_0835 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QQQ1, superoxide dismutase |
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-Cytochrome c oxidase ... , 3 types, 3 molecules TRU
| #6: Protein | Mass: 15177.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4267 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R056, cytochrome-c oxidase |
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| #7: Protein | Mass: 64162.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: D806_022970 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A2U9PNL2, cytochrome-c oxidase |
| #9: Protein | Mass: 8365.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_4693 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R1B6 |
-Non-polymers , 18 types, 336 molecules 
































| #13: Chemical | Mass: 1415.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C72H135O24P #14: Chemical | #15: Chemical | ChemComp-MQ9 / #16: Chemical | ChemComp-CDL / #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-7PH / ( #20: Chemical | |
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Mycolicibacterium smegmatis (bacteria)
Sweden, 1items
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