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- PDB-7t2r: Structure of electron bifurcating Ni-Fe hydrogenase complex HydAB... -
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Basic information
Entry | Database: PDB / ID: 7t2r | |||||||||
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Title | Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state | |||||||||
![]() | (NiFe hydrogenase ...) x 5 | |||||||||
![]() | OXIDOREDUCTASE / hydrogenase complex / electron bifurcation | |||||||||
Function / homology | ![]() ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Feng, X. / Li, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase. Authors: Xiang Feng / Gerrit J Schut / Dominik K Haja / Michael W W Adams / Huilin Li / ![]() Abstract: Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents ...Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents the fourth group, but its bifurcation site is unknown. We report cryo-EM structures of the related NiFe-HydABCSL hydrogenase that reversibly oxidizes H and couples endergonic reduction of ferredoxin with exergonic reduction of NAD. FMN surrounded by a unique arrangement of iron sulfur clusters forms the bifurcating center. NAD binds to FMN in HydB, and electrons from H via HydA to a HydB [4Fe-4S] cluster enable the FMN to reduce NAD. Low-potential electron transfer from FMN to the HydC [2Fe-2S] cluster and subsequent reduction of a uniquely penta-coordinated HydB [2Fe-2S] cluster require conformational changes, leading to ferredoxin binding and reduction by a [4Fe-4S] cluster in HydB. This work clarifies the electron transfer pathways for a large group of hydrogenases underlying many essential functions in anaerobic microorganisms. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 641.1 KB | Display | ![]() |
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PDB format | ![]() | 534.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 25633MC ![]() 7t30C 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
-NiFe hydrogenase ... , 5 types, 10 molecules AFBGCHDIEJ
#1: Protein | Mass: 76799.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 65557.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 17482.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 53294.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 19965.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 4 types, 22 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/3NI.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/3NI.gif)
![](data/chem/img/FCO.gif)
#6: Chemical | ChemComp-FES / #7: Chemical | ChemComp-SF4 / #8: Chemical | #9: Chemical | |
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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: NiFe hydrogenase complex ABCSL / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.5 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm |
Image recording | Electron dose: 76 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 269151 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |