+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9610 | |||||||||||||||||||||
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Title | Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis | |||||||||||||||||||||
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Sample |
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Function / homology | Function and homology information aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / : ...aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / respiratory electron transport chain / electron transport chain / aerobic respiration / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Mycobacterium smegmatis MC2 51 (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Xu A / Gong HR / Ji WX / Gao RG / Wang SH / Li J / Wang Q / Rao ZH | |||||||||||||||||||||
Funding support | China, 6 items
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Citation | Journal: Science / Year: 2018 Title: An electron transfer path connects subunits of a mycobacterial respiratory supercomplex. Authors: Hongri Gong / Jun Li / Ao Xu / Yanting Tang / Wenxin Ji / Ruogu Gao / Shuhui Wang / Lu Yu / Changlin Tian / Jingwen Li / Hsin-Yung Yen / Sin Man Lam / Guanghou Shui / Xiuna Yang / Yuna Sun / ...Authors: Hongri Gong / Jun Li / Ao Xu / Yanting Tang / Wenxin Ji / Ruogu Gao / Shuhui Wang / Lu Yu / Changlin Tian / Jingwen Li / Hsin-Yung Yen / Sin Man Lam / Guanghou Shui / Xiuna Yang / Yuna Sun / Xuemei Li / Minze Jia / Cheng Yang / Biao Jiang / Zhiyong Lou / Carol V Robinson / Luet-Lok Wong / Luke W Guddat / Fei Sun / Quan Wang / Zihe Rao / Abstract: We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from It comprises a complex III dimer flanked on either side by individual complex IV ...We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from It comprises a complex III dimer flanked on either side by individual complex IV subunits. Complex III and IV associate so that electrons can be transferred from quinol in complex III to the oxygen reduction center in complex IV by way of a bridging cytochrome subunit. We observed a superoxide dismutase-like subunit at the periplasmic face, which may be responsible for detoxification of superoxide formed by complex III. The structure reveals features of an established drug target and provides a foundation for the development of treatments for human tuberculosis. | |||||||||||||||||||||
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_9610.map.gz | 88.9 MB | EMDB map data format | |
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Header (meta data) | emd-9610-v30.xml emd-9610.xml | 33.1 KB 33.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9610_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_9610.png | 169.3 KB | ||
Masks | emd_9610_msk_1.map | 95 MB | Mask map | |
Others | emd_9610_half_map_1.map.gz emd_9610_half_map_2.map.gz | 72.8 MB 72.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9610 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9610 | HTTPS FTP |
-Validation report
Summary document | emd_9610_validation.pdf.gz | 738.6 KB | Display | EMDB validaton report |
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Full document | emd_9610_full_validation.pdf.gz | 738.1 KB | Display | |
Data in XML | emd_9610_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_9610_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9610 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9610 | HTTPS FTP |
-Related structure data
Related structure data | 6adqMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9610.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3 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_9610_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_9610_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_9610_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Superoxide dismutase in complex with bcc-aa3 type CIII-CIV superc...
+Supramolecule #1: Superoxide dismutase in complex with bcc-aa3 type CIII-CIV superc...
+Macromolecule #1: Cytochrome c oxidase subunit 2
+Macromolecule #2: Cytochrome c oxidase subunit 1
+Macromolecule #3: Cytochrome c oxidase subunit 3
+Macromolecule #4: Cytochrome c oxidase polypeptide 4
+Macromolecule #5: Cytochrome c oxidase subunit CtaJ
+Macromolecule #6: Uncharacterized protein MSMEG_4692/MSMEI_4575
+Macromolecule #7: Prokaryotic respiratory supercomplex associate factor 1 PRSAF1
+Macromolecule #8: Superoxide dismutase [Cu-Zn]
+Macromolecule #9: LpqE protein
+Macromolecule #10: Ubiquinol-cytochrome c reductase cytochrome b subunit
+Macromolecule #11: Cytochrome bc1 complex cytochrome c subunit
+Macromolecule #12: Rieske iron-sulfur protein QcrA
+Macromolecule #13: COPPER (II) ION
+Macromolecule #14: HEME-A
+Macromolecule #15: CARDIOLIPIN
+Macromolecule #16: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)...
+Macromolecule #17: PALMITIC ACID
+Macromolecule #18: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
+Macromolecule #19: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3...
+Macromolecule #20: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #21: MENAQUINONE-9
+Macromolecule #22: HEME C
+Macromolecule #23: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 46.4 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6adq: |