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Yorodumi- PDB-7nkz: Cryo-EM structure of the cytochrome bd oxidase from M. tuberculos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nkz | |||||||||||||||
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Title | Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution | |||||||||||||||
Components | (Probable integral membrane cytochrome D ubiquinol oxidase (Subunit ...) x 2 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / Terminal oxidase Oxidoreductase Oxygen reductase bd oxidase | |||||||||||||||
Function / homology | Function and homology information cytochrome complex / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / membrane => GO:0016020 / electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||||||||
Authors | Safarian, S. / Wu, D. / Krause, K.L. / Michel, H. | |||||||||||||||
Funding support | Germany, New Zealand, 4items
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Citation | Journal: Nat Commun / Year: 2021 Title: The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB. Authors: Schara Safarian / Helen K Opel-Reading / Di Wu / Ahmad R Mehdipour / Kiel Hards / Liam K Harold / Melanie Radloff / Ian Stewart / Sonja Welsch / Gerhard Hummer / Gregory M Cook / Kurt L ...Authors: Schara Safarian / Helen K Opel-Reading / Di Wu / Ahmad R Mehdipour / Kiel Hards / Liam K Harold / Melanie Radloff / Ian Stewart / Sonja Welsch / Gerhard Hummer / Gregory M Cook / Kurt L Krause / Hartmut Michel / Abstract: New drugs are urgently needed to combat the global TB epidemic. Targeting simultaneously multiple respiratory enzyme complexes of Mycobacterium tuberculosis is regarded as one of the most effective ...New drugs are urgently needed to combat the global TB epidemic. Targeting simultaneously multiple respiratory enzyme complexes of Mycobacterium tuberculosis is regarded as one of the most effective treatment options to shorten drug administration regimes, and reduce the opportunity for the emergence of drug resistance. During infection and proliferation, the cytochrome bd oxidase plays a crucial role for mycobacterial pathophysiology by maintaining aerobic respiration at limited oxygen concentrations. Here, we present the cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 Å. In conjunction with atomistic molecular dynamics (MD) simulation studies we discovered a previously unknown MK-9-binding site, as well as a unique disulfide bond within the Q-loop domain that defines an inactive conformation of the canonical quinol oxidation site in Actinobacteria. Our detailed insights into the long-sought atomic framework of the cytochrome bd oxidase from M. tuberculosis will form the basis for the design of highly specific drugs to act on this enzyme. | |||||||||||||||
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 | 7nkz.cif.gz | 148.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nkz.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 7nkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nkz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7nkz_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7nkz_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 7nkz_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/7nkz ftp://data.pdbj.org/pub/pdb/validation_reports/nk/7nkz | HTTPS FTP |
-Related structure data
Related structure data | 12451MC 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
-Probable integral membrane cytochrome D ubiquinol oxidase (Subunit ... , 2 types, 2 molecules BA
#1: Protein | Mass: 37650.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: cydB, Rv1622c Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) Strain (production host): mc2 155 / Variant (production host): delta cydAB / References: UniProt: O06139 |
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#2: Protein | Mass: 53863.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: cydA, Rv1623c Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) Strain (production host): mc2 155 / Variant (production host): delta cydAB / References: UniProt: L7N662 |
-Non-polymers , 5 types, 47 molecules
#3: Chemical | ChemComp-OXY / | ||
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#4: Chemical | ChemComp-MQ9 / | ||
#5: Chemical | ChemComp-HDD / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-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: Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.0915 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Plasmid: pYUB28b | |||||||||||||||
Buffer solution | pH: 7 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Monodisperse sample of cytochrome bd oxidase reconstituted in lipid nanodiscs 1D1 | |||||||||||||||
Specimen support | Details: 15 mA / Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blot force 20 |
-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 / Calibrated magnification: 96000 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5 sec. / Electron dose: 15 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12070 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 15000000 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 843799 / Algorithm: EXACT BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 70 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||
Atomic model building |
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