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Yorodumi- EMDB-30943: Cryo-EM structure of apo hybrid respiratory supercomplex consisti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30943 | ||||||||||||||||||
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Title | Cryo-EM structure of apo hybrid respiratory supercomplex consisting of Mycobacterium tuberculosis complexIII and Mycobacterium smegmatis complexIV | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | Function and homology information aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / : / respiratory electron transport chain / peptidoglycan-based cell wall / electron transport chain / 2 iron, 2 sulfur cluster binding ...aerobic electron transport chain / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / : / respiratory electron transport chain / peptidoglycan-based cell wall / electron transport chain / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Mycolicibacterium smegmatis MC2 51 (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria) / Mycobacterium smegmatis MC2 51 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.68 Å | ||||||||||||||||||
Authors | Zhou S / Wang W / Gao Y / Gong H / Rao Z | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: Elife / Year: 2021 Title: Structure of cytochrome in complex with Q203 and TB47, two anti-TB drug candidates. Authors: Shan Zhou / Weiwei Wang / Xiaoting Zhou / Yuying Zhang / Yuezheng Lai / Yanting Tang / Jinxu Xu / Dongmei Li / Jianping Lin / Xiaolin Yang / Ting Ran / Hongming Chen / Luke W Guddat / Quan ...Authors: Shan Zhou / Weiwei Wang / Xiaoting Zhou / Yuying Zhang / Yuezheng Lai / Yanting Tang / Jinxu Xu / Dongmei Li / Jianping Lin / Xiaolin Yang / Ting Ran / Hongming Chen / Luke W Guddat / Quan Wang / Yan Gao / Zihe Rao / Hongri Gong / Abstract: Pathogenic mycobacteria pose a sustained threat to global human health. Recently, cytochrome complexes have gained interest as targets for antibiotic drug development. However, there is currently no ...Pathogenic mycobacteria pose a sustained threat to global human health. Recently, cytochrome complexes have gained interest as targets for antibiotic drug development. However, there is currently no structural information for the cytochrome complex from these pathogenic mycobacteria. Here, we report the structures of cytochrome alone (2.68 Å resolution) and in complex with clinical drug candidates Q203 (2.67 Å resolution) and TB47 (2.93 Å resolution) determined by single-particle cryo-electron microscopy. cytochrome forms a dimeric assembly with endogenous menaquinone/menaquinol bound at the quinone/quinol-binding pockets. We observe Q203 and TB47 bound at the quinol-binding site and stabilized by hydrogen bonds with the side chains of Thr and Glu, residues that are conserved across pathogenic mycobacteria. These high-resolution images provide a basis for the design of new mycobacterial cytochrome inhibitors that could be developed into broad-spectrum drugs to treat mycobacterial infections. | ||||||||||||||||||
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_30943.map.gz | 484.1 MB | EMDB map data format | |
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Header (meta data) | emd-30943-v30.xml emd-30943.xml | 27.3 KB 27.3 KB | Display Display | EMDB header |
Images | emd_30943.png | 165.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30943 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30943 | HTTPS FTP |
-Validation report
Summary document | emd_30943_validation.pdf.gz | 529.1 KB | Display | EMDB validaton report |
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Full document | emd_30943_full_validation.pdf.gz | 528.7 KB | Display | |
Data in XML | emd_30943_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_30943_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30943 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30943 | HTTPS FTP |
-Related structure data
Related structure data | 7e1vMC 7e1wC 7e1xC 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_30943.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : apo hybrid respiratory supercomplex consisting of Mycobacterium t...
+Supramolecule #1: apo hybrid respiratory supercomplex consisting of Mycobacterium t...
+Supramolecule #2: Mycobacterium tuberculosis complexIII
+Supramolecule #3: Mycobacterium smegmatis complexIV
+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: Cytochrome bc1 complex cytochrome b subunit
+Macromolecule #9: Cytochrome bc1 complex Rieske iron-sulfur subunit
+Macromolecule #10: Cytochrome bc1 complex cytochrome c subunit
+Macromolecule #11: COPPER (II) ION
+Macromolecule #12: CARDIOLIPIN
+Macromolecule #13: PALMITIC ACID
+Macromolecule #14: HEME-A
+Macromolecule #15: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)...
+Macromolecule #16: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #17: MENAQUINONE-9
+Macromolecule #18: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #19: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3...
+Macromolecule #20: HEME C
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 1.8 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112804 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |