9GTI | pdb_00009gti

X-ray crystal structure of mouse NPTN N-terminal domain

PDB DOI: https://doi.org/10.2210/pdb9GTI/pdb

Classification: CELL ADHESION
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-09-17 Released: 2025-08-06
Deposition Author(s): Vinayagam, D., Raunser, S., Sistel, O., Shulte, U., Constantin, C.E., Prubaum, D., Zolles, G., Fakler, B.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.248 (Depositor), 0.259 (DCC)
R-Value Work:
0.215 (Depositor), 0.227 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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 646: 236-245

PubMed: 40836084 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 75.18 kDa
Atom Count: 4,059
Modeled Residue Count: 473
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroplastin	A, B, C, D	161	Mus musculus	Mutation(s): 0 Gene Names: Nptn, Sdfr1, Sdr1
UniProt & NIH Common Fund Data Resources
Find proteins for P97300 (Mus musculus) Explore P97300 Go to UniProtKB: P97300
IMPC: MGI:108077
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P97300
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE (Subject of Investigation/LOI) Query on EPE Download Ideal Coordinates CCD File SDF format, chain T [auth D] MOL2 format, chain T [auth D] mmCIF format, chain T [auth D]	T [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain T [auth D] Interactions & Density Focus chain T [auth D]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D]