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- EMDB-12209: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -
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Open data
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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) | |||||||||||||||
![]() | Composite map of the dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei | |||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Pfeil-Gardiner O / Watanabe T / Shima S / Murphy BJ | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() Title: New tool: phenix.real_space_refine Authors: Afonine PV / Headd JJ / Terwilliger TC / Adams PD | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 246.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.1 KB 32.1 KB | Display Display | ![]() |
Images | ![]() | 128.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bkcMC ![]() 7bkbC ![]() 7bkdC ![]() 7bkeC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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 | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.6 / Component - Concentration: 25.0 mM / Component - Formula: Tris-HCl![]() ![]() |
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) |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
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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![]() 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: |