2CM6

crystal structure of the C2B domain of rabphilin3A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The C2A-C2B Linker Defines the High Affinity Ca2+ Binding Mode of Rabphilin-3A.

Montaville, P.Schlicker, C.Leonov, A.Zweckstetter, M.Sheldrick, G.M.Becker, S.

(2007) J.Biol.Chem. 282: 5015

  • DOI: 10.1074/jbc.M606746200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Ca(2+) binding properties of C2 domains are essential for the function of their host proteins. We present here the first crystal structures showing an unexpected Ca(2+) binding mode of the C2B domain of rabphilin-3A in atomic detail. Acidic resid ...

    The Ca(2+) binding properties of C2 domains are essential for the function of their host proteins. We present here the first crystal structures showing an unexpected Ca(2+) binding mode of the C2B domain of rabphilin-3A in atomic detail. Acidic residues from the linker region between the C2A and C2B domains of rabphilin-3A interact with the Ca(2+)-binding region of the C2B domain. Because of these interactions, the coordination sphere of the two bound Ca(2+) ions is almost complete. Mutation of these acidic residues to alanine resulted in a 10-fold decrease in the intrinsic Ca(2+) binding affinity of the C2B domain. Using NMR spectroscopy, we show that this interaction occurred only in the Ca(2+)-bound state of the C2B domain. In addition, this Ca(2+) binding mode was maintained in the C2 domain tandem fragment. In NMR-based liposome binding assays, the linker was not released upon phospholipid binding. Therefore, this unprecedented Ca(2+) binding mode not only shows how a C2 domain increases its intrinsic Ca(2+) affinity, but also provides the structural base for an atypical protein-Ca(2+)-phospholipid binding mode of rabphilin-3A.


    Organizational Affiliation

    Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, University of Göttingen, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RABPHILIN-3A
A, B
166Rattus norvegicusMutation(s): 0 
Gene Names: Rph3a
Find proteins for P47709 (Rattus norvegicus)
Go to UniProtKB:  P47709
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.268 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.069α = 90.00
b = 59.606β = 103.89
c = 66.385γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance