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- PDB-8jp0: structure of human sodium-calciumexchanger NCX1 -

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Basic information

Entry
Database: PDB / ID: 8jp0
Titlestructure of human sodium-calciumexchanger NCX1
ComponentsSodium/calcium exchanger 1
KeywordsTRANSPORT PROTEIN / sodium/calcium exchanger / membrane protein
Function / homology
Function and homology information


relaxation of smooth muscle / vascular associated smooth muscle contraction / negative regulation of intracellular signal transduction / calcium:sodium antiporter activity / regulation of cell communication by electrical coupling / calcium ion export / membrane depolarization during cardiac muscle cell action potential / regulation of the force of heart contraction / cell communication by electrical coupling involved in cardiac conduction / sodium ion export across plasma membrane ...relaxation of smooth muscle / vascular associated smooth muscle contraction / negative regulation of intracellular signal transduction / calcium:sodium antiporter activity / regulation of cell communication by electrical coupling / calcium ion export / membrane depolarization during cardiac muscle cell action potential / regulation of the force of heart contraction / cell communication by electrical coupling involved in cardiac conduction / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / calcium ion import / calcium ion transport into cytosol / relaxation of cardiac muscle / cardiac muscle cell development / regulation of cardiac muscle contraction by calcium ion signaling / Sodium/Calcium exchangers / ankyrin binding / Reduction of cytosolic Ca++ levels / cellular response to caffeine / negative regulation of cytosolic calcium ion concentration / calcium ion transmembrane import into cytosol / positive regulation of the force of heart contraction / calcium ion import across plasma membrane / intercalated disc / regulation of cardiac conduction / positive regulation of bone mineralization / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / cytoskeletal protein binding / cardiac muscle contraction / Ion homeostasis / monoatomic ion transport / response to muscle stretch / axon terminus / T-tubule / sodium ion transmembrane transport / muscle contraction / regulation of heart rate / cell periphery / cellular response to reactive oxygen species / sarcolemma / calcium ion transmembrane transport / Z disc / intracellular calcium ion homeostasis / regulation of gene expression / transmembrane transporter binding / calmodulin binding / postsynapse / postsynaptic density / axon / neuronal cell body / dendrite / calcium ion binding / synapse / nucleoplasm / plasma membrane
Similarity search - Function
Sodium/calcium exchanger, isoform 1 / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region ...Sodium/calcium exchanger, isoform 1 / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / DnaJ domain
Similarity search - Domain/homology
Chem-EKY / Sodium/calcium exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDong, Y. / Zhao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
National Natural Science Foundation of China (NSFC)92157102 China
CitationJournal: EMBO J / Year: 2024
Title: Structural insight into the allosteric inhibition of human sodium-calcium exchanger NCX1 by XIP and SEA0400.
Authors: Yanli Dong / Zhuoya Yu / Yue Li / Bo Huang / Qinru Bai / Yiwei Gao / Qihao Chen / Na Li / Lingli He / Yan Zhao /
Abstract: Sodium-calcium exchanger proteins influence calcium homeostasis in many cell types and participate in a wide range of physiological and pathological processes. Here, we elucidate the cryo-EM ...Sodium-calcium exchanger proteins influence calcium homeostasis in many cell types and participate in a wide range of physiological and pathological processes. Here, we elucidate the cryo-EM structure of the human Na/Ca exchanger NCX1.3 in the presence of a specific inhibitor, SEA0400. Conserved ion-coordinating residues are exposed on the cytoplasmic face of NCX1.3, indicating that the observed structure is stabilized in an inward-facing conformation. We show how regulatory calcium-binding domains (CBDs) assemble with the ion-translocation transmembrane domain (TMD). The exchanger-inhibitory peptide (XIP) is trapped within a groove between the TMD and CBD2 and predicted to clash with gating helices TMs at the outward-facing state, thus hindering conformational transition and promoting inactivation of the transporter. A bound SEA0400 molecule stiffens helix TM2ab and affects conformational rearrangements of TM2ab that are associated with the ion-exchange reaction, thus allosterically attenuating Ca-uptake activity of NCX1.3.
History
DepositionJun 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/calcium exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1662
Polymers104,7941
Non-polymers3711
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium/calcium exchanger 1 / Na(+)/Ca(2+)-exchange protein 1 / Solute carrier family 8 member 1


Mass: 104794.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC8A1, CNC, NCX1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P32418
#2: Chemical ChemComp-EKY / 2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline


Mass: 371.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19F2NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Human sodium/calcium exchenger 1(NCX1), monomer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
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 / Nominal defocus max: 22000 nm / Nominal defocus min: 12000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177782 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045803
ELECTRON MICROSCOPYf_angle_d0.6877873
ELECTRON MICROSCOPYf_dihedral_angle_d13.223773
ELECTRON MICROSCOPYf_chiral_restr0.048899
ELECTRON MICROSCOPYf_plane_restr0.006985

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