8SGI | pdb_00008sgi

Cryo-EM structure of human NCX1 in complex with SEA0400

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens, Mus musculus
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2023-04-12 Released: 2024-04-24 
  • Deposition Author(s): Xue, J., Jiang, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural mechanisms of PIP 2 activation and SEA0400 inhibition in human cardiac sodium-calcium exchanger NCX1.

Xue, J.Zeng, W.John, S.Attiq, N.Ottolia, M.Jiang, Y.

(2025) Elife 14

  • DOI: https://doi.org/10.7554/eLife.105396
  • Primary Citation of Related Structures:  
    8SGI, 9IV8

  • PubMed Abstract: 

    Na + /Ca 2+ exchangers (NCXs) transport Ca 2+ across the plasma membrane in exchange for Na + and play a vital role in maintaining cellular Ca 2+ homeostasis. Our previous structural study of human cardiac NCX1 (HsNCX1) reveals the overall architecture of the eukaryotic exchanger and the formation of the inactivation assembly by the intracellular regulatory domain that underlies the cytosolic Na + -dependent inactivation and Ca 2+ activation of NCX1. Here, we present the cryo-EM structures of HsNCX1 in complex with a physiological activator phosphatidylinositol 4,5-bisphosphate (PIP 2 ), or pharmacological inhibitor SEA0400, that enhances the inactivation of the exchanger. We demonstrate that PIP 2 binding stimulates NCX1 activity by inducing a conformational change at the interface between the transmembrane (TM) and cytosolic domains that destabilizes the inactivation assembly. In contrast, SEA0400 binding in the TM domain of NCX1 stabilizes the exchanger in an inward-facing conformation that facilitates the formation of the inactivation assembly, thereby promoting the Na + -dependent inactivation of NCX1. Thus, this study reveals the structural basis of PIP 2 activation and SEA0400 inhibition of NCX1 and provides some mechanistic understandings of cellular regulation and pharmacology of NCX family proteins.


  • Organizational Affiliation
    • Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/calcium exchanger 1982Homo sapiensMutation(s): 0 
Gene Names: SLC8A1CNCNCX1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P32418 (Homo sapiens)
Explore P32418 
Go to UniProtKB:  P32418
PHAROS:  P32418
GTEx:  ENSG00000183023 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32418
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainB [auth L]202Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainC [auth H]249Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EKY (Subject of Investigation/LOI)
Query on EKY

Download Ideal Coordinates CCD File 
D [auth A]2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline
C21 H19 F2 N O3
YSUBLPUJDOWYDP-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM140892
Welch FoundationUnited StatesI-1578
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-03-05
    Changes: Data collection, Database references
  • Version 1.3: 2025-04-09
    Changes: Data collection, Database references
  • Version 1.4: 2025-05-28
    Changes: Data collection
  • Version 1.5: 2025-06-04
    Changes: Data collection, Database references