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- EMDB-51546: Mouse PMCA-NPTN complex captured in E1-ATP state without calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-51546
TitleMouse PMCA-NPTN complex captured in E1-ATP state without calcium
Map data
Sample
  • Complex: PMCA-NPTN complex prepared in the presence of ATP analog
    • Protein or peptide: Plasma membrane calcium-transporting ATPase 2
    • Protein or peptide: Neuroplastin
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • 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: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / 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
Neuroplastin / Plasma membrane calcium-transporting ATPase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 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: 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 CE / Prumbaum D / Zolles G / Fakler B
History
DepositionSep 15, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51546.png

Downloads & links

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Map

FileDownload / File: emd_51546.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.56
Minimum - Maximum-2.4315238 - 3.657297
Average (Standard dev.)0.003473094 (±0.07676778)
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_51546_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51546_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PMCA-NPTN complex prepared in the presence of ATP analog

EntireName: PMCA-NPTN complex prepared in the presence of ATP analog
Components
  • Complex: PMCA-NPTN complex prepared in the presence of ATP analog
    • Protein or peptide: Plasma membrane calcium-transporting ATPase 2
    • Protein or peptide: Neuroplastin
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • 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: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PMCA-NPTN complex prepared in the presence of ATP analog

SupramoleculeName: PMCA-NPTN complex prepared in the presence of ATP analog
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: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: (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: 5 / 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 #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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.3 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: 5788 / Average exposure time: 3.0 sec. / Average electron dose: 59.0 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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Software - details: non uniform refinement / Number images used: 185466
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: 133.2
Output model

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

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