+
Open data
-
Basic information
Entry | Database: PDB / ID: 6a69 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a P-type ATPase | ||||||
![]() |
| ||||||
![]() | STRUCTURAL PROTEIN / Membrane protein | ||||||
Function / homology | ![]() P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration / regulation of receptor localization to synapse / calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / : / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of vascular associated smooth muscle contraction / type 1 fibroblast growth factor receptor binding / : / excitatory synapse assembly ...P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration / regulation of receptor localization to synapse / calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / : / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of vascular associated smooth muscle contraction / type 1 fibroblast growth factor receptor binding / : / excitatory synapse assembly / cellular response to corticosterone stimulus / : / dendrite self-avoidance / positive regulation of fibroblast growth factor receptor signaling pathway / inhibitory synapse / positive regulation of long-term neuronal synaptic plasticity / GABA receptor activation / cell-cell adhesion mediator activity / P-type Ca2+ transporter / neural retina development / P-type calcium transporter activity / cellular response to vitamin D / ATPase-coupled monoatomic cation transmembrane transporter activity / positive regulation of calcium ion transport / dendritic spine membrane / Reduction of cytosolic Ca++ levels / negative regulation of cytokine production / positive regulation of protein localization / neuronal cell body membrane / negative regulation of cytosolic calcium ion concentration / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules / Ion transport by P-type ATPases / immunological synapse / regulation of cardiac conduction / GABA-ergic synapse / positive regulation of bone mineralization / regulation of cellular response to insulin stimulus / Ion homeostasis / monoatomic ion transmembrane transport / cell adhesion molecule binding / regulation of cytosolic calcium ion concentration / response to cold / positive regulation of long-term synaptic potentiation / PDZ domain binding / long-term synaptic potentiation / axon guidance / Schaffer collateral - CA1 synapse / visual learning / brain development / cytoplasmic side of plasma membrane / regulation of blood pressure / positive regulation of neuron projection development / intracellular calcium ion homeostasis / presynaptic membrane / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / positive regulation of protein phosphorylation / membrane raft / apical plasma membrane / axon / intracellular membrane-bounded organelle / glutamatergic synapse / dendrite / cell surface / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.11 Å | ||||||
![]() | Gong, D.S. / Chi, X.M. / Ren, K. / Huang, G.X.Y. / Zhou, G.W. / Yan, N. / Lei, J.L. / Zhou, Q. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 194.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 149.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 856.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 868.1 KB | Display | |
Data in XML | ![]() | 37.3 KB | Display | |
Data in CIF | ![]() | 56.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6987MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 140987.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Protein | Mass: 31328.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Sugar | ChemComp-NAG / |
Sequence details | THIS SEQUENCE OF NPTN CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: complex of one PMCA1 molecular with one NPTN molecular Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105188 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|