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Yorodumi- PDB-7bkc: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -
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-Basic information
Entry | Database: PDB / ID: 7bkc | |||||||||||||||
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Title | Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (dimeric, composite structure) | |||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / methanogenesis / flavin-based electron bifurcation / CO2-fixation / formate dehydrogenase | |||||||||||||||
Function / homology | Function and homology information formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / methanogenesis, from carbon dioxide / formate metabolic process / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity ...formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / methanogenesis, from carbon dioxide / formate metabolic process / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdopterin cofactor binding / iron-sulfur cluster binding / transition metal ion 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: 3 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. #1: Journal: Comput. Cryst. Newsl. / Year: 2013 Title: New tool: phenix.real_space_refine Authors: Afonine, P.V. / Headd, J.J. / Terwilliger, T.C. / Adams, P.D. | |||||||||||||||
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 | 7bkc.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7bkc.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7bkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/7bkc ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bkc | HTTPS FTP |
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-Related structure data
Related structure data | 12209MC 7bkbC 7bkdC 7bkeC 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 , 5 types, 10 molecules AaFfEeDdIi
#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 #2: Protein | Mass: 15692.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ0 #3: Protein | Mass: 45639.895 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FRK1, formate dehydrogenase #7: Protein | Mass: 28696.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FRL8, formylmethanofuran dehydrogenase |
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-CoB--CoM heterodisulfide reductase subunit ... , 2 types, 4 molecules CcBb
#4: 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 #5: 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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-Formylmethanofuran dehydrogenase, subunit ... , 5 types, 12 molecules LlGgJjMKmkHh
#8: Protein | Mass: 16388.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FKZ5, formylmethanofuran dehydrogenase #9: Protein | Mass: 63636.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FRL9, formylmethanofuran dehydrogenase #10: Protein | Mass: 15157.499 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FRF6, formylmethanofuran dehydrogenase #11: Protein | Mass: 42216.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FKZ4, formylmethanofuran dehydrogenase #12: Protein | Mass: 49371.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) References: UniProt: Q2FRM0, formylmethanofuran dehydrogenase |
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-Non-polymers , 7 types, 68 molecules
#13: Chemical | ChemComp-SF4 / #14: Chemical | ChemComp-FAD / #15: Chemical | #16: Chemical | ChemComp-9S8 / #17: Chemical | ChemComp-ZN / #18: Chemical | #19: Chemical | ChemComp-MGD / |
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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-#12 / 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-HClTris / Formula: Tris-HClTris |
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) |
Specimen support | Details: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 |
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 FIELDBright-field microscopy / 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 | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||||||||||
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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: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1239454 Details: As this is a composite map, the resolution is estimated from the resolutions for masked refinements of several regions, which range from 2.6 to 3.7 A. Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.67 Å2 / Biso mean: 46.8325 Å2 / Biso min: 6.51 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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