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- EMDB-30471: 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30471 | |||||||||
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Title | 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane | |||||||||
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![]() | proton pump / ubiquinol / oxidase / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / 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 / proton transmembrane transporter activity / ubiquinone binding / : ...cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / 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 / proton transmembrane transporter activity / ubiquinone binding / : / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.55 Å | |||||||||
![]() | Li J / Han L | |||||||||
![]() | ![]() 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 | ![]() | 168.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.8 KB 14.8 KB | Display Display | ![]() |
Images | ![]() | 41.4 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cubMC ![]() 7cuqC ![]() 7cuwC ![]() 7n9zC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Cytochrome bo(3) ubiquinol oxidase
+Supramolecule #1: Cytochrome bo(3) ubiquinol oxidase
+Macromolecule #1: Cytochrome bo(3) ubiquinol oxidase subunit 1
+Macromolecule #2: Cytochrome bo(3) ubiquinol oxidase subunit 2
+Macromolecule #3: Cytochrome bo(3) ubiquinol oxidase subunit 3
+Macromolecule #4: Cytochrome bo(3) ubiquinol oxidase subunit 4
+Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #6: HEME O
+Macromolecule #7: COPPER (II) ION
+Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #9: Ubiquinone-8
+Macromolecule #10: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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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: 1.3 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: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 193845 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |