9GQO

Structure of a Ca2+ bound phosphoenzyme intermediate in the inward-to-outward transition of Ca2+-ATPase 1 from Listeria monocytogenes

Summary for 9GQO

• Entry DOI: 10.2210/pdb9gqo/pdb
• EMDB information: 51510
• Descriptor: Calcium-transporting ATPase lmo0841, CALCIUM ION, MAGNESIUM ION (3 entities in total)
• Functional Keywords: membrane protein, intermediate, p-type atpase, calcium transport
• Biological source: Listeria monocytogenes
• Total number of polymer chains: 1
• Total formula weight: 99480.80

Authors

Hansen, S.B.,Flygaard, R.F.,Kjaergaard, M.,Nissen, P. (deposition date: 2024-09-09, release date: 2024-10-16, Last modification date: 2025-06-25)

Primary citation

Basse Hansen, S.,Flygaard, R.K.,Kjaergaard, M.,Nissen, P.
Structure of the [Ca]E2P intermediate of Ca 2+ -ATPase 1 from Listeria monocytogenes.
Embo Rep., 26:1709-1723, 2025

PubMed Abstract: Active transport by P-type Ca-ATPases maintain internal calcium stores and a low cytosolic calcium concentration. Structural studies of mammalian sarco/endoplasmic reticulum Ca-ATPases (SERCA) have revealed several steps of the transport cycle, but a calcium-releasing intermediate has remained elusive. Single-molecule FRET studies of the bacterial Ca-ATPase LMCA1 revealed an intermediate of the transition between so-called [Ca]E1P and E2P states and suggested that calcium release from this intermediate was the essentially irreversible step of transport. Here, we present a 3.5 Å resolution cryo-EM structure for a four-glycine insertion mutant of LMCA1 in a lipid nanodisc obtained under conditions with calcium and ATP and adopting such an intermediate state, denoted [Ca]E2P. The cytosolic domains are positioned in the E2P-like conformation, while the calcium-binding transmembrane (TM) domain adopts a calcium-bound E1P-ADP-like conformation. Missing density for the E292 residue at the calcium site (the equivalent of SERCA1a E309) suggests flexibility and a site poised for calcium release and proton uptake. The structure suggests a mechanism where ADP release and re-organization of the cytoplasmic domains precede calcium release.

PubMed: 40016426
DOI: 10.1038/s44319-025-00392-x

Experimental method

ELECTRON MICROSCOPY (3.46 Å)