Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex

Key Points:

• Extended Data Fig. 1 details the coordination environment of metal clusters in NifDK, identifying key amino acid residues involved in M-cluster and P-cluster ligation, and confirms the presence of the homocitrate cofactor through mass spectrometry and fragmentation analysis.
• Extended Data Fig. 2 and 3 compare structural features and interface interactions of the three NifDK heterotetramers and their interaction with the NifI complex across the supercomplex units, highlighting variations in buried surface areas.
• Extended Data Fig. 4 and 5 analyze ligand binding pockets and structural overlays of the NifI complexes, comparing them with the Glnk structure and illustrating conserved ligand interactions and T-loop conformations.
• Extended Data Figs. 6-8 present structural characterizations of different states of the NifD and NifK complexes (D*KKD*, DKK, and PII-DKKD*), showing electron density maps, cluster coordination, and ADP binding, with notable dynamic regions and structural similarities to the supercomplex.
• Extended Data Fig. 9 uses mass photometry to analyze NifDK complexes under various conditions, revealing the presence of NifDK tetramers, supercomplexes, and smaller complexes influenced by ligand binding and sample concentration.