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- PDB-9gsf: Mouse PMCA-NPTN complex captured in E1-ATP state without calcium -

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Basic information

Entry
Database: PDB / ID: 9gsf
TitleMouse PMCA-NPTN complex captured in E1-ATP state without calcium
Components
  • Neuroplastin
  • Plasma membrane calcium-transporting ATPase 2
KeywordsMEMBRANE PROTEIN / Calcium pump / Ptype-Atpase
Function / homology
Function and homology information


otolith mineralization / regulation of receptor localization to synapse / cerebellar Purkinje cell layer morphogenesis / type 1 fibroblast growth factor receptor binding / inner ear receptor cell differentiation / Reduction of cytosolic Ca++ levels / cGMP metabolic process / cerebellar granule cell differentiation / Ion transport by P-type ATPases / calcium-dependent ATPase activity ...otolith mineralization / regulation of receptor localization to synapse / cerebellar Purkinje cell layer morphogenesis / type 1 fibroblast growth factor receptor binding / inner ear receptor cell differentiation / Reduction of cytosolic Ca++ levels / cGMP metabolic process / cerebellar granule cell differentiation / Ion transport by P-type ATPases / calcium-dependent ATPase activity / excitatory synapse assembly / cerebellar Purkinje cell differentiation / positive regulation of fibroblast growth factor receptor signaling pathway / photoreceptor ribbon synapse / positive regulation of long-term neuronal synaptic plasticity / P-type Ca2+ transporter / detection of mechanical stimulus involved in sensory perception of sound / P-type calcium transporter activity / serotonin metabolic process / Ion homeostasis / positive regulation of calcium ion transport / locomotion / auditory receptor cell stereocilium organization / dendritic spine membrane / negative regulation of cytokine production / inner ear morphogenesis / regulation of cell size / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / cochlea development / immunological synapse / neuromuscular process controlling balance / regulation of cytosolic calcium ion concentration / lactation / cell adhesion molecule binding / cerebellum development / PDZ domain binding / locomotory behavior / establishment of localization in cell / sensory perception of sound / synapse organization / modulation of chemical synaptic transmission / cell morphogenesis / positive regulation of neuron projection development / regulation of synaptic plasticity / long-term synaptic potentiation / neuron cellular homeostasis / positive regulation of protein phosphorylation / intracellular calcium ion homeostasis / neuron differentiation / calcium ion transport / positive regulation of cytosolic calcium ion concentration / presynaptic membrane / basolateral plasma membrane / neuron projection / calmodulin binding / postsynaptic density / cilium / apical plasma membrane / neuronal cell body / dendrite / calcium ion binding / glutamatergic synapse / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase ...Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / Immunoglobulin domain / haloacid dehalogenase-like hydrolase / Immunoglobulin I-set / Immunoglobulin I-set domain / HAD superfamily / HAD-like superfamily / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-KXP / Neuroplastin / Plasma membrane calcium-transporting ATPase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsVinayagam, D. / Raunser, S. / Sistel, O. / Schulte, U. / Constantin, C.E. / Prumbaum, 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: To Be Published
Title: Cryo-EM structure of PMCA-NPTN complex captured in E1-ATP state
Authors: vinayagam, D. / Raunser, S. / Sistel, O. / Schulte, U. / Constantin, C.E. / Prumbaum, D. / Zolles, G. / Fakler, B.
History
DepositionSep 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasma membrane calcium-transporting ATPase 2
B: Neuroplastin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,99211
Polymers181,0872
Non-polymers2,9059
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Plasma membrane calcium-transporting ATPase 2 / PMCA2 / Plasma membrane calcium ATPase isoform 2 / Plasma membrane calcium pump isoform 2


Mass: 134647.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Atp2b2, Pmca2 / Cell line (production host): tsA201 / Production host: Homo sapiens (human) / References: UniProt: Q9R0K7, P-type Ca2+ transporter
#2: Protein Neuroplastin / Stromal cell-derived receptor 1 / SDR-1


Mass: 46440.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nptn, Sdfr1, Sdr1 / Cell line (production host): tsA201 / Production host: Homo sapiens (human) / References: UniProt: P97300

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Sugars , 1 types, 6 molecules

#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 3 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical 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


Mass: 1047.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H85O19P3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PMCA-NPTN complex prepared in the presence of ATP analog
Type: COMPLEX
Details: prepared as separate cDNAs for transient (co)transfection of tsA201 nptn/basi double KO cells
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: Tris 20mM NaCl 150mM
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The complex was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 55000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 113 K / Temperature (min): 93 K
Image recordingAverage exposure time: 3 sec. / Electron dose: 59 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5788
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.7particle selection
2EPUimage acquisitionAFIS
4CTFFIND4CTF correction
7Coot9model fitting
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
11RELION3.1classification
12cryoSPARC43D reconstructionnon uniform refinement
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185466 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 133.2 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6A69
Accession code: 6A69 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.35 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049369
ELECTRON MICROSCOPYf_angle_d0.63612719
ELECTRON MICROSCOPYf_dihedral_angle_d6.3721394
ELECTRON MICROSCOPYf_chiral_restr0.0441507
ELECTRON MICROSCOPYf_plane_restr0.0051595

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