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Yorodumi- EMDB-12209: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12209 | |||||||||||||||
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Title | Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (dimeric, composite structure) | |||||||||||||||
Map data | Composite map of the dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei | |||||||||||||||
Sample |
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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 / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / CoB--CoM heterodisulfide reductase activity / formate metabolic process / methanogenesis, from carbon dioxide / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis ...formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / CoB--CoM heterodisulfide reductase activity / formate metabolic process / methanogenesis, from carbon dioxide / 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 | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Pfeil-Gardiner O / Watanabe T / Shima S / Murphy BJ | |||||||||||||||
Funding support | Germany, Japan, 4 items
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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 PV / Headd JJ / Terwilliger TC / Adams PD | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12209.map.gz | 246.2 MB | EMDB map data format | |
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Header (meta data) | emd-12209-v30.xml emd-12209.xml | 32.1 KB 32.1 KB | Display Display | EMDB header |
Images | emd_12209.png | 128.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12209 | HTTPS FTP |
-Related structure data
Related structure data | 7bkcMC 7bkbC 7bkdC 7bkeC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12209.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of the dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Dimeric formate dehydrogenase - heterodisulfide reductase - formy...
+Supramolecule #1: Dimeric formate dehydrogenase - heterodisulfide reductase - formy...
+Macromolecule #1: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
+Macromolecule #2: F420-non-reducing hydrogenase subunit D
+Macromolecule #3: Formate dehydrogenase, beta subunit (F420)
+Macromolecule #4: CoB--CoM heterodisulfide reductase subunit C
+Macromolecule #5: CoB--CoM heterodisulfide reductase subunit B
+Macromolecule #6: Formate dehydrogenase
+Macromolecule #7: Formylmethanofuran dehydrogenase
+Macromolecule #8: Formylmethanofuran dehydrogenase, subunit G
+Macromolecule #9: Formylmethanofuran dehydrogenase, subunit A
+Macromolecule #10: Formylmethanofuran dehydrogenase, subunit D
+Macromolecule #11: Formylmethanofuran dehydrogenase, subunit F
+Macromolecule #12: Formylmethanofuran dehydrogenase, subunit B
+Macromolecule #13: IRON/SULFUR CLUSTER
+Macromolecule #14: FLAVIN-ADENINE DINUCLEOTIDE
+Macromolecule #15: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #16: Non-cubane [4Fe-4S]-cluster
+Macromolecule #17: ZINC ION
+Macromolecule #18: MOLYBDENUM ATOM
+Macromolecule #19: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.6 / Component - Concentration: 25.0 mM / Component - Formula: Tris-HClTris / Component - Name: Tris-HClTris |
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: 15mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER |
Details | Preparation in an anaerobic tent (O2 < 20 ppm at all times, nearly always < 2ppm) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8745 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software: (Name: CTFFIND (ver. 4.1.13), RELION (ver. 3.1)) |
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Startup model | Type of model: OTHER Details: ab initio model generation, stochastic gradient descent, Relion 3 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) 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. Number images used: 1239454 |
Details | Recorded in counted mode |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-7bkc: |