2YGG

Complex of CaMBR and CaM

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of Human Na+/H+ Exchanger Nhe1 Regulatory Region in Complex with Cam and Ca2+

Koester, S., Pavkov-Keller, T., Kuehlbrandt, W., Yildiz, O.

(2011) J Biol Chem 286: 40954

  • DOI: 10.1074/jbc.M111.286906
  • Primary Citation of Related Structures:  
    2YGG

  • PubMed Abstract: 

    • The ubiquitous mammalian Na(+)/H(+) exchanger NHE1 has critical functions in regulating intracellular pH, salt concentration, and cellular volume. The regulatory C-terminal domain of NHE1 is linked to the ion-translocating N-terminal membrane domain and acts as a scaffold for signaling complexes ...

    The ubiquitous mammalian Na(+)/H(+) exchanger NHE1 has critical functions in regulating intracellular pH, salt concentration, and cellular volume. The regulatory C-terminal domain of NHE1 is linked to the ion-translocating N-terminal membrane domain and acts as a scaffold for signaling complexes. A major interaction partner is calmodulin (CaM), which binds to two neighboring regions of NHE1 in a strongly Ca(2+)-dependent manner. Upon CaM binding, NHE1 is activated by a shift in sensitivity toward alkaline intracellular pH. Here we report the 2.23 Å crystal structure of the NHE1 CaM binding region (NHE1(CaMBR)) in complex with CaM and Ca(2+). The C- and N-lobes of CaM bind the first and second helix of NHE1(CaMBR), respectively. Both the NHE1 helices and the Ca(2+)-bound CaM are elongated, as confirmed by small angle x-ray scattering analysis. Our x-ray structure sheds new light on the molecular mechanisms of the phosphorylation-dependent regulation of NHE1 and enables us to propose a model of how Ca(2+) regulates NHE1 activity.

    Organizational Affiliation: 

    Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SODIUM/HYDROGEN EXCHANGER 1A70Homo sapiensMutation(s): 0 
Gene Names: SLC9A1, APNH1, NHE1
UniProt & NIH Common Fund Data Resources
Find proteins for P19634 (Homo sapiens)
Explore P19634 
Go to UniProtKB:  P19634
PHAROS:  P19634
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19634
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CALMODULINB150Rattus norvegicusMutation(s): 0 
Gene Names: Calm1, Calm, Cam, Cam1, CaMI
UniProt
Find proteins for P0DP29 (Rattus norvegicus)
Explore P0DP29 
Go to UniProtKB:  P0DP29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP29
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAM
Query on TAM
Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
K [auth B]		TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N		 Ligand Interaction
MRD
Query on MRD
Download Ideal Coordinates CCD File 
I [auth B](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
C [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
G [auth B],
H [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.7α = 90
b = 38.35β = 91.35
c = 34.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2011-11-30
    Changes: Database references
  • Version 1.2: 2014-11-19
    Changes: Data collection