2YGG

Complex of CaMBR and CaM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.227 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SODIUM/HYDROGEN EXCHANGER 1
A
70Homo sapiensMutation(s): 0 
Gene Names: SLC9A1 (APNH1, NHE1)
Find proteins for P19634 (Homo sapiens)
Go to Gene View: SLC9A1
Go to UniProtKB:  P19634
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CALMODULIN
B
150Rattus norvegicusMutation(s): 0 
Gene Names: Calm1 (Calm, Cam, Cam1, CaMI)
Find proteins for P0DP29 (Rattus norvegicus)
Go to UniProtKB:  P0DP29
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
TAM
Query on TAM

Download SDF File 
Download CCD File 
A, B
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.227 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 200.700α = 90.00
b = 38.350β = 91.35
c = 34.100γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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