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Yorodumi- PDB-8oh9: Cryo-EM structure of the electron bifurcating transhydrogenase St... -
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-Basic information
Entry | Database: PDB / ID: 8oh9 | |||||||||
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Title | Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 1) | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / flavin based Electron-bifurcation / transhydrogenases / anaerobic metabolism | |||||||||
Function / homology | Function and homology information hydrogen dehydrogenase / hydrogen dehydrogenase activity / formate dehydrogenase / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Sporomusa ovata DSM 2662 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Kumar, A. / Kremp, F. / Mueller, V. / Schuller, J.M. | |||||||||
Funding support | European Union, Germany, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Molecular architecture and electron transfer pathway of the Stn family transhydrogenase. Authors: Anuj Kumar / Florian Kremp / Jennifer Roth / Sven A Freibert / Volker Müller / Jan M Schuller / Abstract: The challenge of endergonic reduction of NADP using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood- ...The challenge of endergonic reduction of NADP using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oh9.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8oh9.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8oh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oh9_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8oh9_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8oh9_validation.xml.gz | 189 KB | Display | |
Data in CIF | 8oh9_validation.cif.gz | 293.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/8oh9 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/8oh9 | HTTPS FTP |
-Related structure data
Related structure data | 16879MC 8oh5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 12 molecules ADGJBEHKCFIL
#1: Protein | Mass: 18973.877 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sporomusa ovata DSM 2662 (bacteria) / References: UniProt: A0A0U1KYW8 #2: Protein | Mass: 63569.254 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sporomusa ovata DSM 2662 (bacteria) / References: UniProt: A0A0U1KYM9 #3: Protein | Mass: 126488.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sporomusa ovata DSM 2662 (bacteria) / References: UniProt: A0A0U1KYI6 |
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-Non-polymers , 4 types, 56 molecules
#4: Chemical | ChemComp-FES / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-SF4 / #7: Chemical | ChemComp-FAD / |
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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: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata in the oxidised state Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Molecular weight | Value: 0.85 MDa / Experimental value: YES |
Source (natural) | Organism: Sporomusa ovata DSM 2662 (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116573 / Symmetry type: POINT | ||||||||||||||||||||||||
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