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- PDB-9gti: X-ray crystal structure of mouse NPTN N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 9gti
TitleX-ray crystal structure of mouse NPTN N-terminal domain
ComponentsNeuroplastin
KeywordsCELL ADHESION / Ig like domain / cell surface protein / Membrane associated
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of receptor localization to synapse / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / positive regulation of fibroblast growth factor receptor signaling pathway / cell-cell adhesion mediator activity / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse / negative regulation of cytokine production ...trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of receptor localization to synapse / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / positive regulation of fibroblast growth factor receptor signaling pathway / cell-cell adhesion mediator activity / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse / negative regulation of cytokine production / homophilic cell-cell adhesion / immunological synapse / positive regulation of protein localization / presynaptic active zone membrane / cell adhesion molecule binding / axon guidance / synaptic membrane / positive regulation of long-term synaptic potentiation / positive regulation of neuron projection development / synapse organization / visual learning / postsynaptic density membrane / modulation of chemical synaptic transmission / GABA-ergic synapse / Schaffer collateral - CA1 synapse / positive regulation of protein phosphorylation / intracellular calcium ion homeostasis / long-term synaptic potentiation / positive regulation of cytosolic calcium ion concentration / presynaptic membrane / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / axon / dendrite / glutamatergic synapse / cell surface / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Neuroplastin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsVinayagam, D. / Raunser, S. / Sistel, O. / Shulte, U. / Constantin, C.E. / Prubaum, D. / Zolles, G. / Fakler, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)TRR 152/3, number 239283807 project P02 Germany
CitationJournal: Nature / Year: 2025
Title: Molecular mechanism of ultrafast transport by plasma membrane Ca-ATPases.
Authors: Deivanayagabarathy Vinayagam / Oleg Sitsel / Uwe Schulte / Cristina E Constantin / Wout Oosterheert / Daniel Prumbaum / Gerd Zolles / Bernd Fakler / Stefan Raunser /
Abstract: 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 ...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.
History
DepositionSep 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuroplastin
B: Neuroplastin
C: Neuroplastin
D: Neuroplastin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,17620
Polymers73,3464
Non-polymers1,83016
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint56 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.907, 85.907, 163.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein
Neuroplastin / Stromal cell-derived receptor 1 / SDR-1


Mass: 18336.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nptn, Sdfr1, Sdr1 / Plasmid: BacMam / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: P97300
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 30 % (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.03→43.93 Å / Num. obs: 45798 / % possible obs: 99.74 % / Redundancy: 20 % / Biso Wilson estimate: 38.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.047 / Net I/σ(I): 12
Reflection shellResolution: 2.03→2.1 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 4435 / CC1/2: 0.55 / Rpim(I) all: 0.63 / % possible all: 97.83

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERAF-P97300-F1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→43.93 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 2284 5 %
Rwork0.2154 --
obs0.217 45685 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 120 181 4061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083924
X-RAY DIFFRACTIONf_angle_d0.8755278
X-RAY DIFFRACTIONf_dihedral_angle_d16.8891467
X-RAY DIFFRACTIONf_chiral_restr0.055572
X-RAY DIFFRACTIONf_plane_restr0.009672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.070.4061370.37082591X-RAY DIFFRACTION97
2.08-2.120.31591410.30762688X-RAY DIFFRACTION100
2.12-2.180.28851400.26932657X-RAY DIFFRACTION100
2.18-2.240.28481410.24822678X-RAY DIFFRACTION100
2.24-2.30.29821410.29542693X-RAY DIFFRACTION100
2.3-2.370.28021410.23042671X-RAY DIFFRACTION100
2.38-2.460.24351430.21842712X-RAY DIFFRACTION100
2.46-2.560.25341410.22172679X-RAY DIFFRACTION100
2.56-2.670.26931430.19652718X-RAY DIFFRACTION100
2.68-2.820.22061410.19492682X-RAY DIFFRACTION100
2.82-2.990.23841440.22727X-RAY DIFFRACTION100
2.99-3.220.21591420.19442702X-RAY DIFFRACTION100
3.22-3.550.24391460.1982765X-RAY DIFFRACTION100
3.55-4.060.2471440.20052739X-RAY DIFFRACTION100
4.06-5.110.20661460.18192783X-RAY DIFFRACTION100
5.11-43.930.27171530.24232916X-RAY DIFFRACTION100

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