+Open data
-Basic information
Entry | Database: PDB / ID: 7koe | |||||||||
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Title | Electron bifurcating flavoprotein Fix/EtfABCX | |||||||||
Components |
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Keywords | FLAVOPROTEIN/Oxidoreductase / membrane-associated / flavin based electron bifurcation / FLAVOPROTEIN / FLAVOPROTEIN-Oxidoreductase complex | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH group of donors; With a quinone or similar compound as acceptor / iron-sulfur cluster binding / FAD binding / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer activity / iron ion binding Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Feng, X. / Li, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Cryoelectron microscopy structure and mechanism of the membrane-associated electron-bifurcating flavoprotein Fix/EtfABCX. Authors: Xiang Feng / Gerrit J Schut / Gina L Lipscomb / Huilin Li / Michael W W Adams / Abstract: The electron-transferring flavoprotein-menaquinone oxidoreductase ABCX (EtfABCX), also known as FixABCX for its role in nitrogen-fixing organisms, is a member of a family of electron-transferring ...The electron-transferring flavoprotein-menaquinone oxidoreductase ABCX (EtfABCX), also known as FixABCX for its role in nitrogen-fixing organisms, is a member of a family of electron-transferring flavoproteins that catalyze electron bifurcation. EtfABCX enables endergonic reduction of ferredoxin (°' ∼-450 mV) using NADH (°' -320 mV) as the electron donor by coupling this reaction to the exergonic reduction of menaquinone (°' -80 mV). Here we report the 2.9 Å structure of EtfABCX, a membrane-associated flavin-based electron bifurcation (FBEB) complex, from a thermophilic bacterium. EtfABCX forms a superdimer with two membrane-associated EtfCs at the dimer interface that contain two bound menaquinones. The structure reveals that, in contrast to previous predictions, the low-potential electrons bifurcated from EtfAB are most likely directly transferred to ferredoxin, while high-potential electrons reduce the quinone via two [4Fe-4S] clusters in EtfX. Surprisingly, EtfX shares remarkable structural similarity with mammalian [4Fe-4S] cluster-containing ETF ubiquinone oxidoreductase (ETF-QO), suggesting an unexpected evolutionary link between bifurcating and nonbifurcating systems. Based on this structure and spectroscopic studies of a closely related EtfABCX, we propose a detailed mechanism of the catalytic cycle and the accompanying structural changes in this membrane-associated FBEB system. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7koe.cif.gz | 411.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7koe.ent.gz | 333.1 KB | Display | PDB format |
PDBx/mmJSON format | 7koe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7koe_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7koe_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7koe_validation.xml.gz | 76.2 KB | Display | |
Data in CIF | 7koe_validation.cif.gz | 110.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/7koe ftp://data.pdbj.org/pub/pdb/validation_reports/ko/7koe | HTTPS FTP |
-Related structure data
Related structure data | 22973MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Electron transfer flavoprotein, ... , 2 types, 4 molecules AEBF
#1: Protein | Mass: 33003.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1530 / Production host: Pyrococcus furiosus COM1 (archaea) / References: UniProt: Q9X1L6 #2: Protein | Mass: 36801.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_1539 / Production host: Pyrococcus furiosus COM1 (archaea) / References: UniProt: R4P3F4 |
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-Protein , 2 types, 4 molecules CGDH
#3: Protein | Mass: 49040.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_1540 / Production host: Pyrococcus furiosus COM1 (archaea) References: UniProt: R4P168, Oxidoreductases; Acting on the CH-NH group of donors; With a quinone or similar compound as acceptor #4: Protein | Mass: 10730.220 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_1541 / Production host: Pyrococcus furiosus COM1 (archaea) / References: UniProt: R4NRM2 |
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-Non-polymers , 3 types, 12 molecules
#5: Chemical | ChemComp-FAD / #6: Chemical | #7: Chemical | ChemComp-SF4 / |
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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 |
-Sample preparation
Component | Name: octameric complex of electron bifurcating flavoprotein Fix/EtfABCX Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Thermotoga maritima MSB8 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Pyrococcus furiosus COM1 (archaea) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 284 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9096 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2471763 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285377 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |