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Open data
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Basic information
Entry | Database: PDB / ID: 9gsf | |||||||||||||||||||||
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Title | Mouse PMCA-NPTN complex captured in E1-ATP state without calcium | |||||||||||||||||||||
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![]() | MEMBRANE PROTEIN / Calcium pump / Ptype-Atpase | |||||||||||||||||||||
Function / homology | ![]() 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 | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||||||||||||||
![]() | Vinayagam, D. / Raunser, S. / Sistel, O. / Schulte, U. / Constantin, C.E. / Prumbaum, D. / Zolles, G. / Fakler, B. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.3 KB | Display | ![]() |
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PDB format | ![]() | 192.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 64.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 51546MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 134647.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 46440.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 1 types, 6 molecules 
#6: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 3 molecules 




#3: Chemical | ChemComp-ANP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-KXP / ( |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 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 |
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Molecular weight | Value: 0.18 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 / Details: Tris 20mM NaCl 150mM |
Specimen | Conc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The complex was monodisperse |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: 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 |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 113 K / Temperature (min): 93 K |
Image recording | Average 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 optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 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 building | B value: 133.2 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6A69 Accession code: 6A69 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.35 Å Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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