8SGJ

Cryo-EM structure of human NCX1 in apo inactivated state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanisms of the human cardiac sodium-calcium exchanger NCX1.

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

(2023) Nat Commun 14: 6181-6181

  • DOI: https://doi.org/10.1038/s41467-023-41885-4
  • Primary Citation of Related Structures:  
    8SGJ, 8SGT

  • PubMed Abstract: 

    Na + /Ca 2+ exchangers (NCX) transport Ca 2+ in or out of cells in exchange for Na + . They are ubiquitously expressed and play an essential role in maintaining cytosolic Ca 2+ homeostasis. Although extensively studied, little is known about the global structural arrangement of eukaryotic NCXs and the structural mechanisms underlying their regulation by various cellular cues including cytosolic Na + and Ca 2+ . Here we present the cryo-EM structures of human cardiac NCX1 in both inactivated and activated states, elucidating key structural elements important for NCX ion exchange function and its modulation by cytosolic Ca 2+ and Na + . We demonstrate that the interactions between the ion-transporting transmembrane (TM) domain and the cytosolic regulatory domain define the activity of NCX. In the inward-facing state with low cytosolic [Ca 2+ ], a TM-associated four-stranded β-hub mediates a tight packing between the TM and cytosolic domains, resulting in the formation of a stable inactivation assembly that blocks the TM movement required for ion exchange function. Ca 2+ binding to the cytosolic second Ca 2+ -binding domain (CBD2) disrupts this inactivation assembly which releases its constraint on the TM domain, yielding an active exchanger. Thus, the current NCX1 structures provide an essential framework for the mechanistic understanding of the ion transport and cellular regulation of NCX family proteins.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.


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
GTEx:  ENSG00000183023 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32418
Sequence Annotations
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  • Reference Sequence
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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
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  • 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Database references