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- PDB-6lod: Cryo-EM structure of the air-oxidized photosynthetic alternative ... -
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Basic information
Entry | Database: PDB / ID: 6lod | ||||||||||||||||||
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Title | Cryo-EM structure of the air-oxidized photosynthetic alternative complex III from Roseiflexus castenholzii | ||||||||||||||||||
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![]() | PHOTOSYNTHESIS / quinol:electron acceptor oxidoreductase | ||||||||||||||||||
Function / homology | ![]() molybdopterin cofactor 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 | ||||||||||||||||||
![]() | Shi, Y. / Xin, Y.Y. / Wang, C. / Blankenship, R.E. / Sun, F. / Xu, X.L. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from . Authors: Yang Shi / Yueyong Xin / Chao Wang / Robert E Blankenship / Fei Sun / Xiaoling Xu / ![]() ![]() Abstract: Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and ...Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and photosynthetic electron transport chains of bacteria. The coupling mechanism, however, is poorly understood. Here, we report the cryo-EM structures of air-oxidized and dithionite-reduced ACIII from the photosynthetic bacterium at 3.3- and 3.5-Å resolution, respectively. We identified a menaquinol binding pocket and an electron transfer wire comprising six hemes and four iron-sulfur clusters that is capable of transferring electrons to periplasmic acceptors. We detected a proton translocation passage in which three strictly conserved, mid-passage residues are likely essential for coupling the redox-driven proton translocation across the membrane. These results allow us to propose a previously unrecognized coupling mechanism that links the respiratory and photosynthetic functions of ACIII. This study provides a structural basis for further investigation of the energy transformation mechanisms in bacterial photosynthesis and respiration. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 425.6 KB | Display | ![]() |
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PDB format | ![]() | 347.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 65.1 KB | Display | |
Data in CIF | ![]() | 98.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0936MC ![]() 0937C ![]() 6loeC 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 , 4 types, 4 molecules ABCE
#1: Protein | Mass: 26076.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A7NJ87 |
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#2: Protein | Mass: 102515.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A7NJ88 |
#3: Protein | Mass: 53938.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A7NJ89 |
#5: Protein | Mass: 18252.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A7NJ91 |
-Uncharacterized protein ... , 2 types, 2 molecules DF
#4: Protein | Mass: 21070.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A7NJ90 |
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#6: Protein | Mass: 46545.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A7NJ92 |
-Non-polymers , 4 types, 12 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/EL6.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/EL6.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
#7: Chemical | ChemComp-HEC / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-F3S / | |
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-Details
Has ligand of interest | Y |
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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: Air-oxidized alternative complex III / Type: COMPLEX / Entity ID: #1-#4, #6 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | 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: 59 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software | Name: RELION / Version: 3 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 257815 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177489 / Symmetry type: POINT |