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- PDB-6a69: Cryo-EM structure of a P-type ATPase -

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Database: PDB / ID: 6a69
TitleCryo-EM structure of a P-type ATPase
  • NeuroplastinNPTN
  • Plasma membrane calcium-transporting ATPase 1ATP2B1
KeywordsSTRUCTURAL PROTEIN / Membrane protein
Function / homologyImmunoglobulin domain / Plasma membrane calcium-transporting ATPase 1 / P-type ATPase / Immunoglobulin subtype 2 / Immunoglobulin subtype / Cation-transporting P-type ATPase, N-terminal / Cation-transporting P-type ATPase, C-terminal / P-type ATPase, subfamily IIB / Immunoglobulin-like domain / P-type ATPase, A domain superfamily ...Immunoglobulin domain / Plasma membrane calcium-transporting ATPase 1 / P-type ATPase / Immunoglobulin subtype 2 / Immunoglobulin subtype / Cation-transporting P-type ATPase, N-terminal / Cation-transporting P-type ATPase, C-terminal / P-type ATPase, subfamily IIB / Immunoglobulin-like domain / P-type ATPase, A domain superfamily / Immunoglobulin-like fold / P-type ATPase, phosphorylation site / Plasma membrane calcium transporting P-type ATPase, C-terminal / HAD superfamily / P-type ATPase, transmembrane domain superfamily / Neuroplastin / P-type ATPase, cytoplasmic domain N / Immunoglobulin-like domain superfamily / Neurotransmitter receptors and postsynaptic signal transmission / Cation transport ATPase (P-type) / haloacid dehalogenase-like hydrolase / E1-E2 ATPase / Ion transport by P-type ATPases / Ion homeostasis / HAD-like superfamily / Reduction of cytosolic Ca++ levels / Ig-like domain profile. / E1-E2 ATPases phosphorylation site. / Plasma membrane calcium transporter ATPase C terminal / Cation transporter/ATPase, N-terminus / Cation transporting ATPase, C-terminus / calcium-transporting ATPase activity involved in regulation of presynaptic cytosolic calcium ion concentration / regulation of receptor localization to synapse / calcium ion transmembrane transporter activity / calcium ion export across plasma membrane / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / cell-cell adhesion mediator activity / dendritic spine membrane / cellular response to corticosterone stimulus / dendrite self-avoidance / integral component of presynaptic active zone membrane / inhibitory synapse / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / neural retina development / Ca2+-transporting ATPase / cellular response to vitamin D / positive regulation of cellular protein localization / calcium-transporting ATPase activity / neuronal cell body membrane / GABA-ergic synapse / regulation of cardiac conduction / homophilic cell adhesion via plasma membrane adhesion molecules / ion transmembrane transport / cytoplasmic side of plasma membrane / integral component of postsynaptic density membrane / cellular calcium ion homeostasis / long-term synaptic potentiation / visual learning / regulation of cytosolic calcium ion concentration / cell adhesion molecule binding / positive regulation of neuron projection development / response to cold / PDZ domain binding / Schaffer collateral - CA1 synapse / positive regulation of long-term synaptic potentiation / presynaptic membrane / brain development / axon guidance / positive regulation of cytosolic calcium ion concentration / apical plasma membrane / ion channel binding / basolateral plasma membrane / calmodulin binding / aging / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / membrane raft / glutamatergic synapse / axon / dendrite / integral component of plasma membrane / cell surface / extracellular exosome / membrane / ATP binding / plasma membrane / nucleus / metal ion binding / Plasma membrane calcium-transporting ATPase 1 / Neuroplastin
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.11 Å resolution
AuthorsGong, D.S. / Chi, X.M. / Ren, K. / Huang, G.X.Y. / Zhou, G.W. / Yan, N. / Lei, J.L. / Zhou, Q.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the human plasma membrane Ca-ATPase 1 in complex with its obligatory subunit neuroplastin.
Authors: Deshun Gong / Ximin Chi / Kang Ren / Gaoxingyu Huang / Gewei Zhou / Nieng Yan / Jianlin Lei / Qiang Zhou
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 27, 2018 / Release: Sep 19, 2018

Structure visualization

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Deposited unit
A: Plasma membrane calcium-transporting ATPase 1
B: Neuroplastin
hetero molecules

Theoretical massNumber of molelcules
Total (without water)172,5373

  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy, 2D classes show that the complex contains one PMCA1 and one NPTN
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)2030
ΔGint (kcal/M)-9
Surface area (Å2)53420


#1: Protein/peptide Plasma membrane calcium-transporting ATPase 1 / ATP2B1 / PMCA1 / Plasma membrane calcium ATPase isoform 1 / Plasma membrane calcium pump isoform 1

Mass: 140987.844 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: ATP2B1, PMCA1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P20020, Ca2+-transporting ATPase
#2: Protein/peptide Neuroplastin / NPTN / Stromal cell-derived receptor 1 / SDR-1

Mass: 31328.400 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y639
#3: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE

Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: complex of one PMCA1 molecular with one NPTN molecular
Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
1Relion 2.0particle selection
2AutoEMationIIimage acquisition
4gctfCTF correction
7UCSF Chimera1.11model fitting
9Relion 2.0initial Euler assignment
10Relion 2.0final Euler assignment
11Relion 2.0classification
12Relion 2.03D reconstruction
13PHENIX1.12model refinement
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 105188 / Symmetry type: POINT
Least-squares processHighest resolution: 4.11 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0118001
ELECTRON MICROSCOPYf_angle_d1.41710881
ELECTRON MICROSCOPYf_dihedral_angle_d5.9925027
ELECTRON MICROSCOPYf_chiral_restr0.0681313
ELECTRON MICROSCOPYf_plane_restr0.0091373

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