5AFP

Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with rhodopsin kinase peptide from Homo sapiens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Neuronal Calcium Sensor-1 Binds the D2 Dopamine Receptor and G-Protein Coupled Receptor Kinase 1 (Grk1) Peptides Using Different Modes of Interactions.

Pandalaneni, S.Karuppiah, V.Saleem, M.Haynes, L.P.Burgoyne, R.D.Mayans, O.Derrick, J.P.Lian, L.Y.

(2015) J.Biol.Chem. 290: 18744

  • DOI: 10.1074/jbc.M114.627059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Neuronal calcium sensor-1 (NCS-1) is the primordial member of the neuronal calcium sensor family of EF-hand Ca(2+)-binding proteins. It interacts with both the G-protein-coupled receptor (GPCR) dopamine D2 receptor (D2R), regulating its internalizati ...

    Neuronal calcium sensor-1 (NCS-1) is the primordial member of the neuronal calcium sensor family of EF-hand Ca(2+)-binding proteins. It interacts with both the G-protein-coupled receptor (GPCR) dopamine D2 receptor (D2R), regulating its internalization and surface expression, and the cognate kinases GRK1 and GRK2. Determination of the crystal structures of Ca(2+)/NCS-1 alone and in complex with peptides derived from D2R and GRK1 reveals that the differential recognition is facilitated by the conformational flexibility of the C-lobe-binding site. We find that two copies of the D2R peptide bind within the hydrophobic crevice on Ca(2+)/NCS-1, but only one copy of the GRK1 peptide binds. The different binding modes are made possible by the C-lobe-binding site of NCS-1, which adopts alternative conformations in each complex. C-terminal residues Ser-178-Val-190 act in concert with the flexible EF3/EF4 loop region to effectively form different peptide-binding sites. In the Ca(2+)/NCS-1·D2R peptide complex, the C-terminal region adopts a 310 helix-turn-310 helix, whereas in the GRK1 peptide complex it forms an α-helix. Removal of Ser-178-Val-190 generated a C-terminal truncation mutant that formed a dimer, indicating that the NCS-1 C-terminal region prevents NCS-1 oligomerization. We propose that the flexible nature of the C-terminal region is essential to allow it to modulate its protein-binding sites and adapt its conformation to accommodate both ligands. This appears to be driven by the variability of the conformation of the C-lobe-binding site, which has ramifications for the target specificity and diversity of NCS-1.


    Organizational Affiliation

    From the NMR Centre for Structural Biology, Institute of Integrative Biology, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURONAL CALCIUM SENSOR 1
A, B
190Rattus norvegicusMutation(s): 0 
Gene Names: Ncs1 (Flup, Freq)
Find proteins for P62168 (Rattus norvegicus)
Go to UniProtKB:  P62168
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RHODOPSIN KINASE
C, D
25Homo sapiensMutation(s): 0 
Gene Names: GRK1 (RHOK)
EC: 2.7.11.14
Find proteins for Q15835 (Homo sapiens)
Go to Gene View: GRK1
Go to UniProtKB:  Q15835
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.690α = 90.00
b = 93.690β = 92.25
c = 55.710γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references
  • Version 1.2: 2015-08-05
    Type: Database references