9ERK
Cryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii reduced with low potential ferredoxin (consensus map)
Summary for 9ERK
| Entry DOI | 10.2210/pdb9erk/pdb |
| EMDB information | 19919 |
| Descriptor | Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A, FLAVIN MONONUCLEOTIDE, RIBOFLAVIN, ... (11 entities in total) |
| Functional Keywords | anaerobic metabolism, bioenergetics, membrane protein, electron transfer, sodium pumping |
| Biological source | Acetobacterium woodii DSM 1030 More |
| Total number of polymer chains | 6 |
| Total formula weight | 184081.27 |
| Authors | Kumar, A.,Schuller, J.M. (deposition date: 2024-03-23, release date: 2025-03-05, Last modification date: 2025-03-19) |
| Primary citation | Kumar, A.,Roth, J.,Kim, H.,Saura, P.,Bohn, S.,Reif-Trauttmansdorff, T.,Schubert, A.,Kaila, V.R.I.,Schuller, J.M.,Muller, V. Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery. Nat Commun, 16:2302-2302, 2025 Cited by PubMed Abstract: The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD and pumps ions (Na or H) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na-pumping NADH-quinone oxidoreductase (Nqr). By running in reverse, Rnf uses the electrochemical ion gradient to drive ferredoxin reduction with NADH, providing low potential electrons for nitrogenases and CO reductases. Yet, the molecular principles that couple the long-range electron transfer to Na translocation remain elusive. Here, we resolve key functional states along the electron transfer pathway in the Na-pumping Rnf complex from Acetobacterium woodii using redox-controlled cryo-electron microscopy that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster electrostatically attracts Na, and in turn, triggers an inward/outward transition with alternating membrane access driving the Na pump and the reduction of NAD. Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems. PubMed: 40055346DOI: 10.1038/s41467-025-57375-8 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.8 Å) |
Structure validation
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