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Entry
Database: EMDB / ID: EMD-55424
TitleLocal refinement map of the Vhu hydrogenase of the Hdr-Vhu-Fdh complex
Map dataLocal Refinement of the VhuABDG- Hydrogenase
Sample
  • Complex: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
KeywordsMethanogenesis / Super-assembly / Flavin-based electron bifurcation / heterodisulfide-reductase / polyferredoxin / formylmethanofuran dehydrogenase / electron transport / oxidoreductase
Biological speciesMethanococcus maripaludis S2 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsPaul S / Schuller JM
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)505997786 Germany
European Research Council (ERC)101075992European Union
CitationJournal: To Be Published
Title: An eight-megadalton super-assembly links the first and the last step in methanogenesis to power CO2 reduction
Authors: Paul S / Schuller JM
History
DepositionOct 21, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55424.png

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Map

FileReleased
AnnotationLocal Refinement of the VhuABDG- Hydrogenase
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.149
Minimum - Maximum-0.4369699 - 1.5498191
Average (Standard dev.)0.00095121097 (±0.009376559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 760.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55424_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate deh...

EntireName: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
Components
  • Complex: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly

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Supramolecule #1: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate deh...

SupramoleculeName: Composite map of the Heterodisulfide-Vhu Hydrogenase- Formate dehydrogenase complex within the eight-megadalton Hdr-Vhu-Fdh super-assembly
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Methanococcus maripaludis S2 (archaea)
Molecular weightTheoretical: 8 MDa

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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

BufferpH: 7.6
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
12.5 mMMgCl2magnesium chloride
20.0 ?MC27H33N9O15P2flavin adenine dinucleotide
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification under strict anaerobic conditions inside a Coy Lab's vinyl anaerobic chamber (95% N2/ 5% H2).

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 309332
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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