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TitleArchitecture of the 8 MDa Hdr-Vhu-Fwd super-assembly in class I methanogens.
Journal, issue, pagesNature, Year 2026
Publish dateJul 8, 2026
AuthorsSophia Paul / Tomas C Pascoa / Max A Klamke / Stefan Bohn / Frank Abendroth / Darja Deobald / Olalla Vázquez / Sven T Stripp / Jan M Schuller /
PubMed AbstractMethanogens are central to global carbon cycling and among the largest biological sources of methane, a potent greenhouse gas. At the heart of their energy metabolism lies the Hdr-Vhu-Fwd super- ...Methanogens are central to global carbon cycling and among the largest biological sources of methane, a potent greenhouse gas. At the heart of their energy metabolism lies the Hdr-Vhu-Fwd super-assembly, which couples H oxidation with CO reduction through flavin-based electron bifurcation. Here we present the cryogenic electron microscopy structure of the Hdr-Vhu-Fwd super-assembly from Methanococcus maripaludis, revealing an 8 MDa complex comprising 252 polypeptide chains and over 600 redox cofactors. Cryo-electron tomography further support that this super-assembly forms an intact structure within the cytoplasm of intact cells. This architecture comprises two hexameric HdrABC-Vhu rings linked by a tetrameric FwdF core, forming a continuous, circular electron chain. In this unique arrangement, 12 polyferredoxin subunits (VhuB) connect the Vhu-Hdr and Fwd complexes, thereby coupling electron bifurcation with CO reduction and directly linking the last and the first step of methanogenesis. Moreover, we identify a modular variant of the complex in which the [NiFe]-hydrogenase Vhu is substituted by tungsten-containing formate dehydrogenase (FdhAB), indicating flexible integration of electron-input modules facilitating metabolic adaptation under diverse environmental conditions. Analysis of the taxonomic distribution reveals that this architecture is specific to class I methanogens and is distinct from the smaller Hdr-Fmd complex of class II. Together, our study reveals that the the Hdr-Vhu-Fwd super-assembly has a modular and adaptable bioenergetic assembly, suggesting a lineage-specific architecture to adapt to diverse anaerobic niches.
External linksNature / PubMed:42420451
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution3.04 - 11.1 Å
Structure data

54825

9sfi

EMDB-54825, PDB-9sfi:
Heterodisulfide reductase-Formylmethanofuran dehydrogenase super-assembly
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-54996: Consensus map of the eight- megadalton Hdr-Vhu-Fwd super-assembly
Method: EM (single particle) / Resolution: 4.05 Å

EMDB-54997: Local refinement of VhuB from the eight-megadalton Hdr-Vhu-Fwd super-assembly
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-54998: Local refinement of VhuB from the eight-megadalton Hdr-Vhu-Fwd super-assembly, state 2
Method: EM (single particle) / Resolution: 3.19 Å

EMDB-54999: Local Refinement of the HdrABC-dimer from the eight-megadalton Hdr-Vhu-Fwd super-assembly
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-55009: Local refinement of FwdF from the eight-megadalton Hdr-Vhu-Fwd super-assembly
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-55010: Local refinement of the outer FwdABCDG-complex from the eight-megadalton Hdr-Vhu-Fwd super-assembly
Method: EM (single particle) / Resolution: 3.15 Å

EMDB-55423: Local refinement of the inner region of FwdABCDG from the eight mega-dalton Hdr-Vhu-Fwd super-assembly
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-55424: Local refinement map of the Vhu hydrogenase of the Hdr-Vhu-Fdh complex
Method: EM (single particle) / Resolution: 3.41 Å

EMDB-55426: Local refinement map of the formate dehydrogenase of the Hdr-Vhu-Fdh complex
Method: EM (single particle) / Resolution: 3.31 Å

55451

9t1s

EMDB-55451: Composite map of the Hdr-Vhu-Fdh dimer
PDB-9t1s: Heterodisulfide-Hydrogenase-Formate Dehydrogenase dimer
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-58201: In situ subtomogram average of the M. maripaludis Hdr-Vhu-Fwd supercomplex
Method: EM (subtomogram averaging) / Resolution: 11.1 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-ZN:
Unknown entry

ChemComp-MGD:
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

ChemComp-W:
Unknown entry

ChemComp-NFU:
formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)

Source
  • Methanococcus maripaludis S2 (archaea)
  • methanococcus maripaludis (archaea)
  • methanococcus maripaludis deltae (archaea)
KeywordsELECTRON TRANSPORT / Methanogenesis / Super-assembly / Flavin-based elctron bifurcation / Heterodisulfide-reductase / Polyferredoxin / Formylmethanofuran dehydrogenase / Flavin-based electron bifurcation / oxidoreductase

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