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- EMDB-25647: Structure of electron bifurcating Ni-Fe hydrogenase complex HydAB... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-25647 | |||||||||
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Title | Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN/NAD(H) bound state | |||||||||
![]() | Electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN/NAD(H) bound state | |||||||||
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Function / homology | ![]() ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 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 | single particle reconstruction / cryo EM / Resolution: 3.0 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 74 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 82.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t30MC ![]() 7t2rC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN/NAD(H) bound state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : NiFe hydrogenase complex ABCSL
+Supramolecule #1: NiFe hydrogenase complex ABCSL
+Macromolecule #1: NiFe hydrogenase subunit A
+Macromolecule #2: NiFe hydrogenase subunit B
+Macromolecule #3: NiFe hydrogenase subunit C
+Macromolecule #4: NiFe hydrogenase large subunit
+Macromolecule #5: NiFe hydrogenase small subunit
+Macromolecule #6: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #7: IRON/SULFUR CLUSTER
+Macromolecule #8: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #9: FLAVIN MONONUCLEOTIDE
+Macromolecule #10: NICKEL (III) ION
+Macromolecule #11: CARBONMONOXIDE-(DICYANO) IRON
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-7t30: |