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Open data
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Basic information
Entry | Database: PDB / ID: 6klv | |||||||||
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Title | Hyperthermophilic respiratory Complex III | |||||||||
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![]() | OXIDOREDUCTASE / Respiratory chain / Complex III / Hyperthermophilic mechanism / antimycin A | |||||||||
Function / homology | ![]() intracellular organelle / ubiquinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Fei, S. / Hartmut, M. / Yun, Z. / Guohong, P. / Guoliang, Z. / Hui, Z. / Shuangbo, Z. / Xiaoyun, P. / Yan, Z. | |||||||||
![]() | ![]() 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. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.9 KB | Display | ![]() |
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PDB format | ![]() | 245.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0719MC ![]() 0716C ![]() 6klsC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 19429.857 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 47045.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 27680.170 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 17 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/DLX.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AMY.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/DLX.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/AMY.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/HEC.gif)
#4: Chemical | #5: Chemical | ChemComp-DLX / #6: Chemical | ChemComp-HEM / #7: Chemical | #8: Chemical | #9: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: The cytochrome bc1 complex (respiratory complex III) / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81350 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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