3W3A

Crystal structure of V1-ATPase at 3.9 angstrom resolution

Summary for 3W3A

• Entry DOI: 10.2210/pdb3w3a/pdb
• Related: 3A5C 3A5D
• Descriptor: V-type ATP synthase alpha chain, V-type ATP synthase beta chain, V-type ATP synthase subunit D, ... (5 entities in total)
• Functional Keywords: atp synthesis, hydrogen ion transport, nucleotide-binding, catalytic domain, molecular motor proteins, quaternary, proton-translocating atpases, thermus thermophilus, vacuolar proton-translocating atpases, hydrolysis, hydrolase
• Biological source: Thermus thermophilus; More
• Total number of polymer chains: 16
• Total formula weight: 756937.23

Authors

Nagamatsu, Y.,Takeda, K.,Kuranaga, T.,Numoto, N.,Miki, K. (deposition date: 2012-12-14, release date: 2013-05-15, Last modification date: 2024-03-20)

Primary citation

Nagamatsu, Y.,Takeda, K.,Kuranaga, T.,Numoto, N.,Miki, K.
Origin of Asymmetry at the Intersubunit Interfaces of V1-ATPase from Thermusthermophilus
J.Mol.Biol., 425:2699-2708, 2013

PubMed Abstract: V-type ATPase (V-ATPase) is one of the rotary ATPase complexes that mediate energy conversion between the chemical energy of ATP and the ion gradient across the membrane through a rotary catalytic mechanism. Because V-ATPase has structural features similar to those of well-studied F-type ATPase, the structure is expected to highlight the common essence of the torque generation of rotary ATPases. Here, we report a complete model of the extra-membrane domain of the V-ATPase (V1-ATPase) of a thermophilic bacterium, Thermus thermophilus, consisting of three A subunits, three B subunits, one D subunit, and one F subunit. The X-ray structure at 3.9Å resolution provides detailed information about the interactions between A3B3 and DF subcomplexes as well as interactions among the respective subunits, which are defined by the properties of side chains. Asymmetry at the intersubunit interfaces was detected from the structural differences among the three AB pairs in the different reaction states, while the large interdomain motion in the catalytic A subunits was not observed unlike F1 from various species and V1 from Enterococcus hirae. Asymmetry is mainly realized by rigid-body rearrangements of the relative position between A and B subunits. This is consistent with the previous observations by the high-resolution electron microscopy for the whole V-ATPase complexes. Therefore, our result plausibly implies that the essential motion for the torque generation is not the large interdomain movement of the catalytic subunits but the rigid-body rearrangement of subunits.

PubMed: 23639357
DOI: 10.1016/j.jmb.2013.04.022

Experimental method

X-RAY DIFFRACTION (3.9 Å)