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

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Basic information

Entry
Database: PDB / ID: 6a69
TitleCryo-EM structure of a P-type ATPase
Components
  • 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

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Structure visualization

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  • Deposited structure unit
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  • EMDB-6987
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)172,5373
Polyers172,3162
Non-polymers2211
Water0
1


  • 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

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Components

#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
Sequence detailsTHIS SEQUENCE OF NPTN CORRESPONDS TO THE ISOFORM 1 FOUND IN UNP Q9Y639.

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Experimental details

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Experiment

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

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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

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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)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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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