+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60320 | |||||||||
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Title | Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Metyltetraprole / Inhibitor / Complex / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex III / quinol-cytochrome-c reductase ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / hippocampus development / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.53 Å | |||||||||
Authors | Wang YX / Sun JY / Cui GR / Yang GF | |||||||||
Funding support | China, 1 items
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Citation | Journal: J Am Chem Soc / Year: 2024 Title: Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome Complex Enabling Rational Design of Inhibitors. Authors: Yu-Xia Wang / Ying Ye / Zhi-Wen Li / Guang-Rui Cui / Xing-Xing Shi / Ying Dong / Jia-Jia Jiang / Jia-Yue Sun / Ze-Wei Guan / Nan Zhang / Qiong-You Wu / Fan Wang / Xiao-Lei Zhu / Guang-Fu Yang / Abstract: Cytochrome (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QI) that combats ...Cytochrome (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QI) that combats the G143A mutated isolate, which confers high resistance to strobilurin fungicides such as pyraclostrobin (PYR). The binding mode and antiresistance mechanism of MET remain unclear. Here, we determined the high-resolution structures of inhibitor-bound complex III (MET, 2.52 Å; PYR, 2.42 Å) and inhibitor-bound porcine complex III (MET, 2.53 Å; PYR, 2,37 Å) by cryo-electron microscopy. The distinct binding modes of MET and PYR were observed for the first time. Notably, the MET exhibited different binding modes in the two species. In , the binding site of MET was the same as PYR, serving as a -type inhibitor of the Q site. However, in porcine, MET acted as a dual-target inhibitor of both Q and Q. Based on the structural insights, a novel inhibitor (YF23694) was discovered and demonstrated excellent fungicidal activity against downy mildew and powdery mildew fungi. This work provides a new starting point for the design of the next generation of inhibitors to overcome the resistance. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60320.map.gz | 97 MB | EMDB map data format | |
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Header (meta data) | emd-60320-v30.xml emd-60320.xml | 26 KB 26 KB | Display Display | EMDB header |
Images | emd_60320.png | 45.3 KB | ||
Filedesc metadata | emd-60320.cif.gz | 7.4 KB | ||
Others | emd_60320_half_map_1.map.gz emd_60320_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60320 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60320 | HTTPS FTP |
-Validation report
Summary document | emd_60320_validation.pdf.gz | 842.4 KB | Display | EMDB validaton report |
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Full document | emd_60320_full_validation.pdf.gz | 842 KB | Display | |
Data in XML | emd_60320_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_60320_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60320 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60320 | HTTPS FTP |
-Related structure data
Related structure data | 8zowMC 8yhqC 8yinC 8zmtC 8zosC 8zp0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_60320.map.gz / Format: CCP4 / Size: 103 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: 0.96 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60320_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60320_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex
+Supramolecule #1: Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex
+Macromolecule #1: Cytochrome b
+Macromolecule #2: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #3: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #4: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 6
+Macromolecule #7: Cytochrome b-c1 complex subunit 7
+Macromolecule #8: Cytochrome b-c1 complex subunit 8
+Macromolecule #9: Complex III subunit 9
+Macromolecule #10: Cytochrome b-c1 complex subunit 10
+Macromolecule #11: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #12: 1-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]-3-methyl-phenyl]...
+Macromolecule #13: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #14: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #15: CARDIOLIPIN
+Macromolecule #16: HEME C
+Macromolecule #17: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.72 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 411418 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |