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- EMDB-51544: Cryo-EM structure of mouse PMCA-NPTN complex captured in E2 state... -

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Entry
Database: EMDB / ID: EMD-51544
TitleCryo-EM structure of mouse PMCA-NPTN complex captured in E2 state (BEF3)
Map data
Sample
  • Complex: PMCA-NPTN complex captured in E2 state (BEF3)
    • Protein or peptide: Plasma membrane calcium-transporting ATPase 2
    • Protein or peptide: Neuroplastin
  • Ligand: MAGNESIUM ION
  • Ligand: (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
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsCalcium pump / Ptype-Atpase / MEMBRANE PROTEIN
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 / Ion transport by P-type ATPases / cerebellar granule cell differentiation / 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 / Ion transport by P-type ATPases / cerebellar granule cell differentiation / calcium-dependent ATPase activity / cerebellar Purkinje cell differentiation / excitatory synapse assembly / photoreceptor ribbon synapse / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / P-type Ca2+ transporter / P-type calcium transporter activity / detection of mechanical stimulus involved in sensory perception of sound / 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 / neuromuscular process controlling balance / regulation of cell size / homophilic cell-cell adhesion / inner ear development / cochlea development / immunological synapse / regulation of cytosolic calcium ion concentration / cell adhesion molecule binding / lactation / cerebellum development / PDZ domain binding / locomotory behavior / establishment of localization in cell / sensory perception of sound / positive regulation of neuron projection development / synapse organization / neuron cellular homeostasis / regulation of synaptic plasticity / modulation of chemical synaptic transmission / long-term synaptic potentiation / positive regulation of protein phosphorylation / cell morphogenesis / neuron differentiation / intracellular calcium ion homeostasis / calcium ion transport / positive regulation of cytosolic calcium ion concentration / presynaptic membrane / basolateral plasma membrane / calmodulin binding / neuron projection / postsynaptic density / cilium / apical plasma membrane / neuronal cell body / calcium ion binding / dendrite / 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
Neuroplastin / Plasma membrane calcium-transporting ATPase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsVinayagam D / Raunser S / Sistel O / Schulte U / Constantin CE / Prumbaum D / Zolles G / Fakler B
Funding support Germany, 2 items
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 15, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51544.png

Downloads & links

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Map

FileDownload / File: emd_51544.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.528
Minimum - Maximum-3.629278 - 5.9526815
Average (Standard dev.)0.0029829056 (±0.107198484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51544_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_51544_half_map_2.map
Projections & Slices
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Sample components

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Entire : PMCA-NPTN complex captured in E2 state (BEF3)

EntireName: PMCA-NPTN complex captured in E2 state (BEF3)
Components
  • Complex: PMCA-NPTN complex captured in E2 state (BEF3)
    • Protein or peptide: Plasma membrane calcium-transporting ATPase 2
    • Protein or peptide: Neuroplastin
  • Ligand: MAGNESIUM ION
  • Ligand: (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
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: PMCA-NPTN complex captured in E2 state (BEF3)

SupramoleculeName: PMCA-NPTN complex captured in E2 state (BEF3) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: prepared as separate cDNAs for transient (co)transfection of tsA201 nptn/basi double KO cells
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Plasma membrane calcium-transporting ATPase 2

MacromoleculeName: Plasma membrane calcium-transporting ATPase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Ca2+ transporter
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 134.647141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDMTNSDFY SKNQRNESSH GGEFGCTMEE LRSLMELRGT EAVVKIKETY GDTEAICRRL KTSPVEGLPG TAPDLEKRKQ IFGQNFIPP KKPKTFLQLV WEALQDVTLI ILEIAAIISL GLSFYHPPGE SNEGCATAQG GAEDEGEAEA GWIEGAAILL S VICVVLVT ...String:
MGDMTNSDFY SKNQRNESSH GGEFGCTMEE LRSLMELRGT EAVVKIKETY GDTEAICRRL KTSPVEGLPG TAPDLEKRKQ IFGQNFIPP KKPKTFLQLV WEALQDVTLI ILEIAAIISL GLSFYHPPGE SNEGCATAQG GAEDEGEAEA GWIEGAAILL S VICVVLVT AFNDWSKEKQ FRGLQSRIEQ EQKFTVVRAG QVVQIPVAEI VVGDIAQIKY GDLLPADGLF IQGNDLKIDE SS LTGESDQ VRKSVDKDPM LLSGTHVMEG SGRMVVTAVG VNSQTGIIFT LLGAGGEEEE KKDKKAKQQD GAAAMEMQPL KSA EGGDAD DKKKANMHKK EKSVLQGKLT KLAVQIGKAG LVMSAITVII LVLYFTVDTF VVNKKPWLTE CTPVYVQYFV KFFI IGVTV LVVAVPEGLP LAVTISLAYS VKKMMKDNNL VRHLDACETM GNATAICSDK TGTLTTNRMT VVQAYVGDVH YKEIP DPSS INAKTLELLV NAIAINSAYT TKILPPEKEG ALPRQVGNKT ECGLLGFVLD LRQDYEPVRS QMPEEKLYKV YTFNSV RKS MSTVIKMPDE SFRMYSKGAS EIVLKKCCKI LSGAGEARVF RPRDRDEMVK KVIEPMACDG LRTICVAYRD FPSSPEP DW DNENDILNEL TCICVVGIED PVRPEVPEAI RKCQRAGITV RMVTGDNINT ARAIAIKCGI IHPGEDFLCL EGKEFNRR I RNEKGEIEQE RIDKIWPKLR VLARSSPTDK HTLVKGIIDS THTEQRQVVA VTGDGTNDGP ALKKADVGFA MGIAGTDVA KEASDIILTD DNFSSIVKAV MWGRNVYDSI SKFLQFQLTV NVVAVIVAFT GACITQDSPL KAVQMLWVNL IMDTFASLAL ATEPPTETL LLRKPYGRNK PLISRTMMKN ILGHAVYQLT LIFTLLFVGE KMFQIDSGRN APLHSPPSEH YTIIFNTFVM M QLFNEINA RKIHGERNVF DGIFRNPIFC TIVLGTFAIQ IVIVQFGGKP FSCSPLQLDQ WMWCIFIGLG ELVWGQVIAT IP TSRLKFL KEAGRLTQKE EIPEEELNED VEEIDHAERE LRRGQILWFR GLNRIQTQIR VVKAFRSSLY EGLEKPESRT SIH NFMAHP EFRIEDSQPH IPLIDDTDLE EDAALKQNSS PPSSLNKNNS AIDSGINLTT DTSKSATSSS PGSPIHSLET SLEN LYFQG GDYKDDDDK

UniProtKB: Plasma membrane calcium-transporting ATPase 2

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Macromolecule #2: Neuroplastin

MacromoleculeName: Neuroplastin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 46.440059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSSLPGAL ALSLLLVSGS LLPGPGAAQN AGFVKSPMSE TKLTGDAFEL YCDVVGSPTP EIQWWYAEVN RAESFRQLWD GARKRRVTV NTAYGSNGVS VLRITRLTLE DSGTYECRAS NDPKRNDLRQ NPSITWIRAQ ATISVLQKPR IVTSEEVIIR E SLLPVTLQ ...String:
MSGSSLPGAL ALSLLLVSGS LLPGPGAAQN AGFVKSPMSE TKLTGDAFEL YCDVVGSPTP EIQWWYAEVN RAESFRQLWD GARKRRVTV NTAYGSNGVS VLRITRLTLE DSGTYECRAS NDPKRNDLRQ NPSITWIRAQ ATISVLQKPR IVTSEEVIIR E SLLPVTLQ CNLTSSSHTL MYSYWTRNGV ELTATRKNAS NMEYRINKPR AEDSGEYHCV YHFVSAPKAN ATIEVKAAPD IT GHKRSEN KNEGQDAMMY CKSVGYPHPE WIWRKKENGV FEEISNSSGR FFITNKENYT ELSIVNLQIT EDPGEYECNA TNS IGSASV STVLRVRSHL APLWPFLGIL AEIIILVVII VVYEKRKRPD EVPDDDEPAG PMKTNSTNNH KDKNLRQRNT NENL YFQGG HHHHHHHH

UniProtKB: Neuroplastin

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bi...

MacromoleculeName: (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
type: ligand / ID: 4 / Number of copies: 1 / Formula: KXP
Molecular weightTheoretical: 1.047088 KDa
Chemical component information

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

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Macromolecule #5: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 7.4 / Details: Tris 20mM NaCl 150mM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe complex was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 93.0 K / Max: 113.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6226 / Average exposure time: 3.0 sec. / Average electron dose: 60.54 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 55000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6a69

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Software - details: non uniform refinement / Number images used: 325585
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.0) / Details: SGD Algorithm implemented in cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

6a69


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 125.1
Output model

PDB-9gsd:
Cryo-EM structure of mouse PMCA-NPTN complex captured in E2 state (BEF3)

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