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Open data
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Basic information
Entry | Database: PDB / ID: 7n9z | ||||||
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Title | E. coli cytochrome bo3 in MSP nanodisc | ||||||
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Function / homology | ![]() cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vallese, F. / Clarke, O.B. | ||||||
![]() | ![]() 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 | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 449.2 KB | Display | ![]() |
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PDB format | ![]() | 369.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 24265MC ![]() 7cubC ![]() 7cuqC ![]() 7cuwC C: citing same article ( M: map data used to model this data |
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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
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Cytochrome o ubiquinol oxidase, subunit ... , 2 types, 2 molecules FI
#1: Protein | Mass: 74424.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: H4KCU1, ![]() |
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#4: Protein | Mass: 12037.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: I2RK84, ![]() |
-Protein , 2 types, 2 molecules GH
#2: Protein | ![]() Mass: 34947.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#3: Protein | Mass: 22642.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Non-polymers , 9 types, 267 molecules ![](data/chem/img/UQ8.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/HEO.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/HEO.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-UQ8 / | ||||||||||||||
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#6: Chemical | ChemComp-LHG / ![]() #7: Chemical | ![]() #8: Chemical | ChemComp-HEO / | ![]() #9: Chemical | ChemComp-HEM / | ![]() #10: Chemical | ChemComp-CDL / | ![]() #11: Chemical | ChemComp-CU / | ![]() #12: Chemical | ChemComp-ZN / | #13: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Cytochrome bo 3 ubiquinol oxidase / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Buffer component |
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Specimen | Conc.: 2.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1 | ||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94681 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 1FFT Accession code: 1FFT / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Highest resolution: 2.19 Å | ||||||||||||||||||||||||
Refine LS restraints |
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