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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24265 | |||||||||
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Title | E. coli cytochrome bo3 in MSP nanodisc | |||||||||
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![]() | Ubiquinone / Heme-copper Oxidoreductase / Electron transport / Bioenergetics / Proton pump / Membrane protein | |||||||||
Function / homology | ![]() cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / aerobic respiration ...cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / aerobic respiration / membrane => GO:0016020 / copper ion binding / heme binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.19 Å | |||||||||
![]() | Vallese F / Clarke OB | |||||||||
![]() | ![]() Title: Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site. Authors: Jiao Li / Long Han / Francesca Vallese / Ziqiao Ding / Sylvia K Choi / Sangjin Hong / Yanmei Luo / Bin Liu / Chun Kit Chan / Emad Tajkhorshid / Jiapeng Zhu / Oliver Clarke / Kai Zhang / Robert Gennis / ![]() ![]() Abstract: Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) ...Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 242 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.8 KB 24.8 KB | Display Display | ![]() |
Images | ![]() | 412.6 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() ![]() | 241.2 MB 475.8 MB 475.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 918.1 KB | Display | ![]() |
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Full document | ![]() | 917.7 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n9zMC ![]() 7cubC ![]() 7cuqC ![]() 7cuwC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 851.4 Data #1: Unaligned multi-frame micrographs of cyt bo3 in MSP Nanodiscs [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.41385 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_24265_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_24265_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_24265_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Cytochrome bo 3 ubiquinol oxidase
+Supramolecule #1: Cytochrome bo 3 ubiquinol oxidase
+Macromolecule #1: Cytochrome o ubiquinol oxidase, subunit I
+Macromolecule #2: Ubiquinol oxidase subunit 2
+Macromolecule #3: Cytochrome o ubiquinol oxidase
+Macromolecule #4: Cytochrome o ubiquinol oxidase, subunit IV
+Macromolecule #5: Ubiquinone-8
+Macromolecule #6: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #7: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #8: HEME O
+Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #10: CARDIOLIPIN
+Macromolecule #11: COPPER (II) ION
+Macromolecule #12: ZINC ION
+Macromolecule #13: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.6 mg/mL | ||||||
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Buffer | pH: 7.4 / Component:
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Grid | Model: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94681 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |