3GIN | pdb_00003gin

Crystal structure of E454K-CBD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.259 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure and functional analysis of a Ca2+ sensor mutant of the na+/ca2+ exchanger

Chaptal, V.Ottolia, M.Mercado-Besserer, G.Nicoll, D.A.Philipson, K.D.Abramson, J.

(2009) J Biological Chem 284: 14688-14692

  • DOI: https://doi.org/10.1074/jbc.C900037200
  • Primary Citation Related Structures: 
    3GIN

  • PubMed Abstract: 

    The mammalian Na(+)/Ca(2+) exchanger, NCX1.1, serves as the main mechanism for Ca(2+) efflux across the sarcolemma following cardiac contraction. In addition to transporting Ca(2+), NCX1.1 activity is also strongly regulated by Ca(2+) binding to two intracellular regulatory domains, CBD1 and CBD2. The structures of both of these domains have been solved by NMR spectroscopy and x-ray crystallography, greatly enhancing our understanding of Ca(2+) regulation. Nevertheless, the mechanisms by which Ca(2+) regulates the exchanger remain incompletely understood. The initial NMR study showed that the first regulatory domain, CBD1, unfolds in the absence of regulatory Ca(2+). It was further demonstrated that a mutation of an acidic residue involved in Ca(2+) binding, E454K, prevents this structural unfolding. A contradictory result was recently obtained in a second NMR study in which Ca(2+) removal merely triggered local rearrangements of CBD1. To address this issue, we solved the crystal structure of the E454K-CBD1 mutant and performed electrophysiological analyses of the full-length exchanger with mutations at position 454. We show that the lysine substitution replaces the Ca(2+) ion at position 1 of the CBD1 Ca(2+) binding site and participates in a charge compensation mechanism. Electrophysiological analyses show that mutations of residue Glu-454 have no impact on Ca(2+) regulation of NCX1.1. Together, structural and mutational analyses indicate that only two of the four Ca(2+) ions that bind to CBD1 are important for regulating exchanger activity.


  • Organizational Affiliation
    • Department of Physiology and Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA.

Macromolecule Content 

  • Total Structure Weight: 35.2 kDa 
  • Atom Count: 1,896 
  • Modeled Residue Count: 232 
  • Deposited Residue Count: 320 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium/calcium exchanger 1
A, B
160Canis lupus familiarisMutation(s): 1 
Gene Names: SLC8A1
UniProt
Find proteins for P23685 (Canis lupus familiaris)
Explore P23685 
Go to UniProtKB:  P23685
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23685
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.259 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.858α = 90
b = 91.858β = 90
c = 65.59γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary