9ERI

Cryo-EM structure of sodium pumping Rnf complex from Acetobacterium woodii bound to NADH

9ERI の概要

• エントリーDOI: 10.2210/pdb9eri/pdb
• EMDBエントリー: 19915
• 分子名称: Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit A, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, RIBOFLAVIN, ... (11 entities in total)
• 機能のキーワード: bioenergetics, anaerobic cryoem, membrane protein, electron transport, redox-driven sodium pumping
• 由来する生物種: Acetobacterium woodii DSM 1030; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 184583.76

構造登録者

Kumar, A.,Schuller, J.M. (登録日: 2024-03-23, 公開日: 2025-03-05, 最終更新日: 2025-07-02)

主引用文献

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

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: 40055346
DOI: 10.1038/s41467-025-57375-8

実験手法

ELECTRON MICROSCOPY (3.3 Å)