5KND

Crystal structure of the Pi-bound V1 complex

Summary for 5KND

• Entry DOI: 10.2210/pdb5knd/pdb
• Related: 5KNB 5KNC
• Descriptor: V-type sodium ATPase catalytic subunit A, V-type sodium ATPase subunit B, V-type sodium ATPase subunit D, ... (9 entities in total)
• Functional Keywords: p-loop, hydrolase, na(+)-atpase, atp binding
• Biological source: Enterococcus hirae ATCC 9790; More
• Total number of polymer chains: 8
• Total formula weight: 392692.36

Authors

Suzuki, K.,Mizutani, K.,Maruyama, S.,Shimono, K.,Imai, F.L.,Muneyuki, E.,Kakinuma, Y.,Ishizuka-Katsura, Y.,Shirouzu, M.,Yokoyama, S.,Yamato, I.,Murata, T. (deposition date: 2016-06-28, release date: 2016-11-02, Last modification date: 2023-11-08)

Primary citation

Suzuki, K.,Mizutani, K.,Maruyama, S.,Shimono, K.,Imai, F.L.,Muneyuki, E.,Kakinuma, Y.,Ishizuka-Katsura, Y.,Shirouzu, M.,Yokoyama, S.,Yamato, I.,Murata, T.
Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Nat Commun, 7:13235-13235, 2016

PubMed Abstract: V-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae ABDF (V) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V-ATPase rotational mechanism model.

PubMed: 27807367
DOI: 10.1038/ncomms13235

Experimental method

X-RAY DIFFRACTION (2.888 Å)