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Yorodumi- EMDB-12451: Cryo-EM structure of the cytochrome bd oxidase from M. tuberculos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12451 | |||||||||||||||
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Title | Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||||||||
Authors | Safarian S / Wu D / Krause KL / Michel H | |||||||||||||||
Funding support | Germany, New Zealand, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12451.map.gz | 39.3 MB | EMDB map data format | |
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Header (meta data) | emd-12451-v30.xml emd-12451.xml | 24.2 KB 24.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12451_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_12451.png | 135.4 KB | ||
Masks | emd_12451_msk_1.map | 64 MB | Mask map | |
Others | emd_12451_additional_1.map.gz emd_12451_half_map_1.map.gz emd_12451_half_map_2.map.gz | 2.9 MB 44.2 MB 44.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12451 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12451 | HTTPS FTP |
-Validation report
Summary document | emd_12451_validation.pdf.gz | 348 KB | Display | EMDB validaton report |
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Full document | emd_12451_full_validation.pdf.gz | 347.1 KB | Display | |
Data in XML | emd_12451_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_12451_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12451 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12451 | HTTPS FTP |
-Related structure data
Related structure data | 7nkzMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12451.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12451_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened Postprocess map
File | emd_12451_additional_1.map | ||||||||||||
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Annotation | Sharpened Postprocess map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12451_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12451_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the cytochrome bd oxidase from M. tuberculos...
Entire | Name: Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution |
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Components |
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-Supramolecule #1: Cryo-EM structure of the cytochrome bd oxidase from M. tuberculos...
Supramolecule | Name: Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Recombinant plasmid: pYUB28b |
Molecular weight | Experimental: 91.5 KDa |
-Macromolecule #1: Probable integral membrane cytochrome D ubiquinol oxidase (Subuni...
Macromolecule | Name: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit II) CydB (Cytochrome BD-I oxidase subunit II) type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 37.650957 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MVLQELWFGV IAALFLGFFI LEGFDFGVGM LMAPFAHVGM GDPETHRRTA LNTIGPVWDG NEVWLITAGA AIFAAFPGWY ATVFSALYL PLLAILFGMI LRAVAIEWRG KIDDPKWRTG ADFGIAAGSW LPALLWGVAF AILVRGLPVD ANGHVALSIP D VLNAYTLL ...String: MVLQELWFGV IAALFLGFFI LEGFDFGVGM LMAPFAHVGM GDPETHRRTA LNTIGPVWDG NEVWLITAGA AIFAAFPGWY ATVFSALYL PLLAILFGMI LRAVAIEWRG KIDDPKWRTG ADFGIAAGSW LPALLWGVAF AILVRGLPVD ANGHVALSIP D VLNAYTLL GGLATAGLFS LYGAVFIALK TSGPIRDDAY RFAVWLSLPV AGLVAGFGLW TQLAYGKDWT WLVLAVAGCA QA AATVLVW RRVSDGWAFM CTLIVVAAVV VLLFGALYPN LVPSTLNPQW SLTIHNASST PYTLKIMTWV TAFFAPLTVA YQT WTYWVF RQRISAERIP PPTGLARRAP |
-Macromolecule #2: Probable integral membrane cytochrome D ubiquinol oxidase (Subuni...
Macromolecule | Name: Probable integral membrane cytochrome D ubiquinol oxidase (Subunit I) CydA (Cytochrome BD-I oxidase subunit I) type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 53.863098 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MNVVDISRWQ FGITTVYHFI FVPLTIGLAP LIAVMQTLWV VTDNPAWYRL TKFFGKLFLI NFAIGVATGI VQEFQFGMNW SEYSRFVGD VFGAPLAMEG LAAFFFESTF IGLWIFGWNR LPRLVHLACI WIVAIAVNVS AFFIIAANSF MQHPVGAHYN P TTGRAELS ...String: MNVVDISRWQ FGITTVYHFI FVPLTIGLAP LIAVMQTLWV VTDNPAWYRL TKFFGKLFLI NFAIGVATGI VQEFQFGMNW SEYSRFVGD VFGAPLAMEG LAAFFFESTF IGLWIFGWNR LPRLVHLACI WIVAIAVNVS AFFIIAANSF MQHPVGAHYN P TTGRAELS SIVVLLTNNT AQAAFTHTVS GALLTAGTFV AAVSAWWLVR SSTTHADSDT QAMYRPATIL GCWVALAATA GL LFTGDHQ GKLMFQQQPM KMASAESLCD TQTDPNFSVL TVGRQNNCDS LTRVIEVPYV LPFLAEGRIS GVTLQGIRDL QQE YQQRFG PNDYRPNLFV TYWSFRMMIG LMAIPVLFAL IALWLTRGGQ IPNQRWFSWL ALLTMPAPFL ANSAGWVFTE MGRQ PWVVV PNPTGDQLVR LTVKAGVSDH SATVVATSLL MFTLVYAVLA VIWCWLLKRY IVEGPLEHDA EPAAHGAPRD DEVAP LSFA Y |
-Macromolecule #3: OXYGEN MOLECULE
Macromolecule | Name: OXYGEN MOLECULE / type: ligand / ID: 3 / Number of copies: 1 / Formula: OXY |
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Molecular weight | Theoretical: 31.999 Da |
Chemical component information | ChemComp-O2: |
-Macromolecule #4: MENAQUINONE-9
Macromolecule | Name: MENAQUINONE-9 / type: ligand / ID: 4 / Number of copies: 1 / Formula: MQ9 |
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Molecular weight | Theoretical: 785.233 Da |
Chemical component information | ChemComp-MQ9: |
-Macromolecule #5: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
Macromolecule | Name: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / type: ligand / ID: 5 / Number of copies: 1 / Formula: HDD |
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Molecular weight | Theoretical: 632.487 Da |
Chemical component information | ChemComp-HDD: |
-Macromolecule #6: HEME B/C
Macromolecule | Name: HEME B/C / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEB |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ChemComp-HEB: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 42 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||
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Buffer | pH: 7 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: 15 mA | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 20. | |||||||||
Details | Monodisperse sample of cytochrome bd oxidase reconstituted in lipid nanodiscs 1D1 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 12070 / Average exposure time: 5.0 sec. / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |