+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0719 | |||||||||
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Title | Hyperthermophilic respiratory Complex III | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information intracellular organelle / ubiquinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Aquifex aeolicus (bacteria) / Aquifex aeolicus (strain VF5) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Fei S / Hartmut M / Yun Z / Guohong P / Guoliang Z / Hui Z / Shuangbo Z / Xiaoyun P / Yan Z | |||||||||
Citation | Journal: Angew Chem Int Ed Engl / Year: 2020 Title: A 3.3 Å-Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability. Authors: Guoliang Zhu / Hui Zeng / Shuangbo Zhang / Jana Juli / Xiaoyun Pang / Jan Hoffmann / Yan Zhang / Nina Morgner / Yun Zhu / Guohong Peng / Hartmut Michel / Fei Sun / Abstract: Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc complex (Complex III) from ...Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N-terminus of cyt. c was found to greatly enhance the interaction between cyt. b and cyt. c , and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc complex in an extreme thermal environment. | |||||||||
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_0719.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-0719-v30.xml emd-0719.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
Images | emd_0719.png | 99.7 KB | ||
Masks | emd_0719_msk_1.map | 40.6 MB | Mask map | |
Others | emd_0719_half_map_1.map.gz emd_0719_half_map_2.map.gz | 30.3 MB 30.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0719 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0719 | HTTPS FTP |
-Related structure data
Related structure data | 6klvMC 0716C 6klsC 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_0719.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: 1.05 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_0719_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_0719_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_0719_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The cytochrome bc1 complex (respiratory complex III)
+Supramolecule #1: The cytochrome bc1 complex (respiratory complex III)
+Macromolecule #1: Rieske-I iron sulfur protein
+Macromolecule #2: Cytochrome b
+Macromolecule #3: Cytochrome c
+Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #5: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-h...
+Macromolecule #6: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #7: ANTIMYCIN
+Macromolecule #8: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #9: HEME C
-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: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81350 |