9GSF | pdb_00009gsf

Mouse PMCA-NPTN complex captured in E1-ATP state without calcium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanism of ultrafast transport by plasma membrane Ca 2+ -ATPases.

Vinayagam, D.Sitsel, O.Schulte, U.Constantin, C.E.Oosterheert, W.Prumbaum, D.Zolles, G.Fakler, B.Raunser, S.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09402-3
  • Primary Citation of Related Structures:  
    9GSD, 9GSE, 9GSF, 9GSG, 9GSH, 9GSI, 9GSY, 9GTB, 9GTI

  • PubMed Abstract: 

    Tight control of intracellular Ca 2+ levels is fundamental as they are used to control numerous signal transduction pathways 1 . Plasma membrane Ca 2+ -ATPases (PMCAs) have a crucial role in this process by extruding Ca 2+ against a steep concentration gradient from the cytosol to the extracellular space 2 . 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 2 , 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 2+ 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 2 are fundamental for its role as a 'latch' promoting the fast release of Ca 2+ 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 2 -binding site as an unanticipated target for drug-mediated manipulation of intracellular Ca 2+ levels. Our work provides detailed structural insights into the uniquely fast operation of native PMCA-type Ca 2+ pumps and its control by membrane lipids and drugs.


  • Organizational Affiliation
    • Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasma membrane calcium-transporting ATPase 21,214Mus musculusMutation(s): 0 
Gene Names: Atp2b2Pmca2
EC: 7.2.2.10
UniProt
Find proteins for Q9R0K7 (Mus musculus)
Explore Q9R0K7 
Go to UniProtKB:  Q9R0K7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R0K7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neuroplastin413Mus musculusMutation(s): 0 
Gene Names: NptnSdfr1Sdr1
UniProt & NIH Common Fund Data Resources
Find proteins for P97300 (Mus musculus)
Explore P97300 
Go to UniProtKB:  P97300
IMPC:  MGI:108077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97300
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P97300-2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KXP (Subject of Investigation/LOI)
Query on KXP

Download Ideal Coordinates CCD File 
E [auth A](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
C47 H85 O19 P3
CNWINRVXAYPOMW-AUBJPSKUSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
I [auth B]
J [auth B]
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyTRR 152/3, number 239283807 project P02

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references