Methanogens are central to global carbon cycling and among the largest biological sources of methane, a potent greenhouse gas1. At the heart of their energy metabolism lies the Hdr–Vhu–Fwd super-assembly, which couples H2 oxidation with CO2 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 CO2 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 conditions2. 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 II3. 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.
