9NVL

ATPase Hybrid F1 with the ancestral core domains Binding Dwell

Summary for 9NVL

• Entry DOI: 10.2210/pdb9nvl/pdb
• EMDB information: 49839
• Descriptor: ATPase Hybrid F1 with the ancestral core domains Chain A, ATPase Hybrid F1 with the ancestral core domains Chain D, ATP synthase gamma chain, ... (7 entities in total)
• Functional Keywords: single particle, ancestral atpase, electron transport
• Biological source: Bacillus sp. PS3; More
• Total number of polymer chains: 7
• Total formula weight: 363024.26

Authors

Stewart, A.G.,Noji, H.,Sobti, M.,Suzuki, A.K. (deposition date: 2025-03-20, release date: 2025-11-05)

Primary citation

Suzuki, A.K.,Furukawa, R.,Sobti, M.,Brown, S.H.J.,Stewart, A.G.,Akanuma, S.,Ueno, H.,Noji, H.
Functional and structural characterization of F 1 -ATPase with common ancestral core domains in stator ring.
Protein Sci., 34:e70345-e70345, 2025

PubMed Abstract: Extant F-ATPases exhibit diverse rotational stepping behaviors-3-, 6-, or 9-step cycles-yet the evolutionary origin of these patterns remains unclear. Here, we used ancestral sequence reconstruction to infer the catalytic β and non-catalytic α subunits of a putative ancestral F-ATPase. We then fused their functionally critical domains into the thermostable F from Bacillus PS3, yielding a stable chimeric enzyme. Cryo-EM revealed two distinct conformational states-binding and catalytic dwell states-separated by a ~34° rotation of the γ subunit, suggesting a fundamental six-step mechanism akin to that of extant six-stepping F-ATPases. Single-molecule rotation assays with ATP and the slowly hydrolyzed ATP analog ATPγS demonstrated that the chimeric motor is intrinsically a six-stepper, pausing at binding and catalytic dwell positions separated by 32.1°, although the binding dwell is significantly prolonged by an unknown mechanism. These findings indicate that F-ATPase was originally a six-stepper and diversified into 3-, 6- and 9-step forms in evolutionary adaptation. Based on these results, we discuss plausible features of the entire FF complex, along with potential physiological contexts in the last universal common ancestor and related lineages.

PubMed: 41131942
DOI: 10.1002/pro.70345

Experimental method

ELECTRON MICROSCOPY (2.46 Å)