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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
  • Neuroplastin
  • Plasma membrane calcium-transporting ATPase 1
KeywordsSTRUCTURAL PROTEIN / Membrane protein
Function / homology
Function and homology information


calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / regulation of receptor localization to synapse / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / photoreceptor ribbon synapse / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of vascular associated smooth muscle contraction ...calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / regulation of receptor localization to synapse / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / photoreceptor ribbon synapse / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of vascular associated smooth muscle contraction / positive regulation of long-term neuronal synaptic plasticity / P-type Ca2+ transporter / P-type calcium transporter activity / positive regulation of calcium ion transport / GABA receptor activation / Sensory processing of sound by inner hair cells of the cochlea / Reduction of cytosolic Ca++ levels / negative regulation of cytokine production / molecular function inhibitor activity / negative regulation of cytosolic calcium ion concentration / homophilic cell-cell adhesion / Ion transport by P-type ATPases / immunological synapse / regulation of cardiac conduction / positive regulation of bone mineralization / regulation of cytosolic calcium ion concentration / cell adhesion molecule binding / Ion homeostasis / regulation of cellular response to insulin stimulus / axon guidance / cell projection / positive regulation of neuron projection development / regulation of blood pressure / long-term synaptic potentiation / positive regulation of protein phosphorylation / intracellular calcium ion homeostasis / synaptic vesicle membrane / positive regulation of cytosolic calcium ion concentration / presynaptic membrane / monoatomic ion transmembrane transport / basolateral plasma membrane / calmodulin binding / postsynaptic density / axon / intracellular membrane-bounded organelle / glutamatergic synapse / cell surface / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / membrane / plasma membrane
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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain ...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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / 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 / Immunoglobulin domain / P-type ATPase, transmembrane domain superfamily / 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
Plasma membrane calcium-transporting ATPase 1 / Neuroplastin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.11 Å
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 /
Abstract: Plasma membrane Ca-ATPases (PMCAs) are key regulators of global Ca homeostasis and local intracellular Ca dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously ...Plasma membrane Ca-ATPases (PMCAs) are key regulators of global Ca homeostasis and local intracellular Ca dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously unrecognized obligatory subunits of PMCAs that dramatically increase the efficiency of PMCA-mediated Ca clearance. Here, we report the cryo-EM structure of human PMCA1 (hPMCA1) in complex with NPTN at a resolution of 4.1 Å for the overall structure and 3.9 Å for the transmembrane domain. The single transmembrane helix of NPTN interacts with the TM-linker and TM10 of hPMCA1. The subunits are required for the hPMCA1 functional activity. The NPTN-bound hPMCA1 closely resembles the E1-Mg structure of endo(sarco)plasmic reticulum Ca ATPase and the Ca site is exposed through a large open cytoplasmic pathway. This structure provides insight into how the subunits bind to the PMCAs and serves as an important basis for understanding the functional mechanisms of this essential calcium pump family.
History
DepositionJun 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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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
Polymers172,3162
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, 2D classes show that the complex contains one PMCA1 and one NPTN
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2030 Å2
ΔGint-9 kcal/mol
Surface area53420 Å2

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Components

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


Mass: 140987.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP2B1, PMCA1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P20020, EC: 3.6.3.8
#2: Protein Neuroplastin / Stromal cell-derived receptor 1 / SDR-1


Mass: 31328.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y639
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY
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 / 3D 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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 (asymmetric)
3D reconstructionResolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105188 / Symmetry type: POINT
RefinementHighest 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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