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Yorodumi- PDB-7bke: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bke | |||||||||||||||
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Title | Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodisulfide reductase core and mobile arm in conformational state 2, composite structure) | |||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / methanogenesis / flavin-based electron bifurcation / CO2-fixation / formate dehydrogenase | |||||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate metabolic process / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate metabolic process / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Methanospirillum hungatei JF-1 (archaea) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Pfeil-Gardiner, O. / Watanabe, T. / Shima, S. / Murphy, B.J. | |||||||||||||||
Funding support | Germany, Japan, 4items
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Citation | Journal: Science / Year: 2021 Title: Three-megadalton complex of methanogenic electron-bifurcating and CO-fixing enzymes. Authors: Tomohiro Watanabe / Olivia Pfeil-Gardiner / Jörg Kahnt / Jürgen Koch / Seigo Shima / Bonnie J Murphy / Abstract: The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly ...The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly reducing electrons for this reaction are generated by heterodisulfide reductase (Hdr) in complex with hydrogenase or formate dehydrogenase (Fdh) using a flavin-based electron-bifurcation mechanism. Here, we report enzymological and structural characterizations of Fdh-Hdr-Fmd complexes from . The complexes catalyze this reaction using electrons from formate and the reduced form of the electron carrier F. Conformational changes in HdrA mediate electron bifurcation, and polyferredoxin FmdF directly transfers electrons to the CO reduction site, as evidenced by methanofuran-dependent flavin-based electron bifurcation even without free ferredoxin, a diffusible electron carrier between Hdr and Fmd. Conservation of Hdr and Fmd structures suggests that this complex is common among hydrogenotrophic methanogens. | |||||||||||||||
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 | 7bke.cif.gz | 556.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bke.ent.gz | 463.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/7bke ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bke | HTTPS FTP |
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-Related structure data
Related structure data | 12212MC 7bkbC 7bkcC 7bkdC 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
-Protein , 4 types, 5 molecules AaFED
#1: Protein | Mass: 72885.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FKZ1, Oxidoreductases; Acting on a sulfur group of donors #4: Protein | | Mass: 15692.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ0 #5: Protein | | Mass: 45639.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FME3, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors #6: Protein | | Mass: 75911.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FRK1, formate dehydrogenase |
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-CoB--CoM heterodisulfide reductase subunit ... , 2 types, 4 molecules CcBb
#2: Protein | Mass: 21706.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ3 #3: Protein | Mass: 32930.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ2 |
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-Non-polymers , 4 types, 26 molecules
#7: Chemical | ChemComp-SF4 / #8: Chemical | #9: Chemical | ChemComp-9S8 / #10: Chemical | ChemComp-FES / | |
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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: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Molecular weight | Value: 0.948 MDa / Experimental value: NO |
Source (natural) | Organism: Methanospirillum hungatei JF-1 (archaea) / Cellular location: cytoplasm |
Buffer solution | pH: 7.6 |
Buffer component | Conc.: 25 mM / Name: Tris-HCl / Formula: Tris-HCl |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Preparation in an anaerobic tent (O2 < 20 ppm at all times, nearly always < 2ppm) |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 293 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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 8745 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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Image processing | Details: Recorded in counted mode | ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 456268 Details: This applies to the map of the 'mobile arm' in state 2. The uploaded map is composite map. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.27 Å2 / Biso mean: 31.7842 Å2 / Biso min: 5.51 Å2 | ||||||||||||||||||||||||||||||||||||
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