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- PDB-7z0t: Structure of the Escherichia coli formate hydrogenlyase complex (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z0t | ||||||
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Title | Structure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, composite structure) | ||||||
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![]() | MEMBRANE PROTEIN / FHL / group-4 membrane bound hydrogenase / [NiFe] hydrogenase | ||||||
Function / homology | ![]() formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / formate dehydrogenase (NAD+) activity / : / glucose catabolic process / anaerobic electron transport chain / urate catabolic process / molybdopterin cofactor binding ...formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / formate dehydrogenase (NAD+) activity / : / glucose catabolic process / anaerobic electron transport chain / urate catabolic process / molybdopterin cofactor binding / anaerobic respiration / cellular respiration / oxidoreductase activity, acting on NAD(P)H / nickel cation binding / quinone binding / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Steinhilper, R. / Murphy, B.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli. Authors: Ralf Steinhilper / Gabriele Höff / Johann Heider / Bonnie J Murphy / ![]() Abstract: The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase ...The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H during fermentation, its reversibility, allowing H-dependent CO reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 471.9 KB | Display | ![]() |
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PDB format | ![]() | 376.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 75.2 KB | Display | |
Data in CIF | ![]() | 115.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14430MC ![]() 7z0sC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Formate hydrogenlyase subunit ... , 6 types, 6 molecules CEBGFD
#1: Protein | Mass: 64121.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 66589.859 Da / Num. of mol.: 1 / Mutation: internal deca-His-Gly-Ser sequence after Gly83 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 21899.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 28033.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 20336.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 33049.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules A
#7: Protein | Mass: 79465.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P07658, formate dehydrogenase (hydrogenase) |
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-Non-polymers , 6 types, 14 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/6MO.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/6MO.gif)
#8: Chemical | ChemComp-NI / | ||||||
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#9: Chemical | ChemComp-FCO / | ||||||
#10: Chemical | ChemComp-SF4 / #11: Chemical | ChemComp-FE / | #12: Chemical | #13: Chemical | ChemComp-6MO / | |
-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: Escherichia coli formate hydrogenlyase complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: C-flat-2/1 |
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 / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 72 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: OTHER / Num. of particles: 90459 Details: This is a composite map. The maps that constitute this composite map have resolutions between 3.0 and 3.4 A. These have all been determined by FSC 0.143 cut-off. Symmetry type: POINT | ||||||||||||||||||||||||||||||||
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