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- EMDB-12198: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -

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Basic information

Entry
Database: EMDB / ID: EMD-12198
TitleFormate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase from Methanospirillum hungatei, dimeric complex, focused refinement of conformational state 2 of the mobile arm
Map data
Sample
  • Complex: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
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 / 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
F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / FAD dependent oxidoreductase ...F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / : / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / FAD dependent oxidoreductase / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / 4Fe-4S dicluster domain / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
F420-non-reducing hydrogenase subunit D / CoB--CoM heterodisulfide reductase iron-sulfur subunit A / CoB--CoM heterodisulfide reductase subunit B / CoB--CoM heterodisulfide reductase subunit C / Formate dehydrogenase, beta subunit (F420) / Formate dehydrogenase, alpha subunit (F420)
Similarity search - Component
Biological speciesMethanospirillum hungatei JF-1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPfeil-Gardiner O / Watanabe T / Shima S / Murphy BJ
Funding support Germany, Japan, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SH 87/1-1 Germany
Japan Society for the Promotion of Science (JSPS) Japan
Alexander von Humboldt Foundation Germany
CitationJournal: 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
DepositionJan 15, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12198.png

Downloads & links

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Map

FileDownload / File: emd_12198.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 432 pix.
= 361.584 Å		0.84 Å/pix.
x 432 pix.
= 361.584 Å		0.84 Å/pix.
x 432 pix.
= 361.584 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.080816865 - 0.14135301
Average (Standard dev.)5.531736e-05 (±0.002496812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 361.584 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z361.584361.584361.584
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0810.1410.000

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Supplemental data

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Additional map: map generated by density modification using phenix resolve...

Fileemd_12198_additional_1.map
Annotationmap generated by density modification using phenix resolve cryo-EM tool
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_12198_half_map_1.map
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Half map: #2

Fileemd_12198_half_map_2.map
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Sample components

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Entire : Dimeric formate dehydrogenase - heterodisulfide reductase - formy...

EntireName: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
Components
  • Complex: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex

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Supramolecule #1: Dimeric formate dehydrogenase - heterodisulfide reductase - formy...

SupramoleculeName: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea) / Location in cell: cytoplasm
Molecular weightTheoretical: 948 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.6 / Component - Concentration: 25.0 mM / Component - Formula: Tris-HCl / Component - Name: Tris-HCl
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER
DetailsPreparation in an anaerobic tent (O2 < 20 ppm at all times, nearly always < 2ppm)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8745 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsRecorded in counted mode
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1.13), RELION (ver. 3.1))
Startup modelType of model: OTHER
Details: ab initio model generation, stochastic gradient descent, Relion 3
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 456268
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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