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Structure paper

TitleMolecular mechanism of ultrafast transport by plasma membrane Ca-ATPases.
Journal, issue, pagesNature, Vol. 646, Issue 8083, Page 236-245, Year 2025
Publish dateAug 20, 2025
AuthorsDeivanayagabarathy Vinayagam / Oleg Sitsel / Uwe Schulte / Cristina E Constantin / Wout Oosterheert / Daniel Prumbaum / Gerd Zolles / Bernd Fakler / Stefan Raunser /
PubMed AbstractTight control of intracellular Ca levels is fundamental as they are used to control numerous signal transduction pathways. Plasma membrane Ca-ATPases (PMCAs) have a crucial role in this process by ...Tight control of intracellular Ca levels is fundamental as they are used to control numerous signal transduction pathways. Plasma membrane Ca-ATPases (PMCAs) have a crucial role in this process by extruding Ca against a steep concentration gradient from the cytosol to the extracellular space. Although new details of PMCA biology are constantly being uncovered, the structural basis of the most distinguishing features of these pumps, namely, transport rates in the kilohertz range and regulation of activity by the plasma membrane phospholipid PtdIns(4,5)P, has so far remained elusive. Here we present the structures of mouse PMCA2 in the presence and absence of its accessory subunit neuroplastin in eight different stages of its transport cycle. Combined with whole-cell recordings that accurately track PMCA-mediated Ca extrusion in intact cells, these structures enable us to establish the first comprehensive transport model for a PMCA, reveal the role of disease-causing mutations and uncover the structural underpinnings of regulatory PMCA-phospholipid interaction. The transport cycle-dependent dynamics of PtdIns(4,5)P are fundamental for its role as a 'latch' promoting the fast release of Ca and opening a passageway for counter-ions. These actions are required for maintaining the ultra-fast transport cycle. Moreover, we identify the PtdIns(4,5)P-binding site as an unanticipated target for drug-mediated manipulation of intracellular Ca levels. Our work provides detailed structural insights into the uniquely fast operation of native PMCA-type Ca pumps and its control by membrane lipids and drugs.
External linksNature / PubMed:40836084 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.03 - 3.7 Å
Structure data

51544

9gsd

EMDB-51544, PDB-9gsd:
Cryo-EM structure of mouse PMCA-NPTN complex captured in E2 state (BEF3)
Method: EM (single particle) / Resolution: 3.04 Å

51545

9gse

EMDB-51545, PDB-9gse:
Cryo-EM structure of mouse PMCA-NPTN complex captured in E1 state without calcium
Method: EM (single particle) / Resolution: 3.64 Å

51546

9gsf

EMDB-51546, PDB-9gsf:
Mouse PMCA-NPTN complex captured in E1-ATP state without calcium
Method: EM (single particle) / Resolution: 3.35 Å

51547

9gsg

EMDB-51547, PDB-9gsg:
Cryo-EM structure of mouse PMCA-NPTN complex captured in E2-Pi state (ALF4)
Method: EM (single particle) / Resolution: 2.83 Å

51548

9gsh

EMDB-51548, PDB-9gsh:
Cryo-EM structure of PMCA-NPTN complex captured in E1-Ca-ATP state
Method: EM (single particle) / Resolution: 3.13 Å

51549

9gsi

EMDB-51549, PDB-9gsi:
Cryo-EM structure of mouse PMCA captured in E1-ATP in the presence of Calcium
Method: EM (single particle) / Resolution: 3.39 Å

51558

9gsy

EMDB-51558, PDB-9gsy:
Cryo-EM structure of mouse PMCA captured in E2-P state (BEF3)
Method: EM (single particle) / Resolution: 3.52 Å

51560

9gtb

EMDB-51560, PDB-9gtb:
Cryo-EM structure of Mouse PMCA-NPTN complex captured in E1-Ca state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-51625: Cryo-EM map of the complete PMCA-NPTN complex captured in E1-Ca state
Method: EM (single particle) / Resolution: 3.7 Å

PDB-9gti:
X-ray crystal structure of mouse NPTN N-terminal domain
Method: X-RAY DIFFRACTION / Resolution: 2.03 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-KXP:
(2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl icosa-5,8,11,14-tetraenoate

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-CA:
Unknown entry

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

Source
  • mus musculus (house mouse)
KeywordsMEMBRANE PROTEIN / Calcium pump / Ptype-Atpase / Calcium Transporter / P-type Atpase / antiporter / CELL ADHESION / Ig like domain / cell surface protein / Membrane associated

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