2CM6 | pdb_00002cm6

crystal structure of the C2B domain of rabphilin3A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.268 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.195 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2CM6

This is version 1.3 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 Biological Chem 282: 5015

  • DOI: https://doi.org/10.1074/jbc.M606746200
  • Primary Citation Related Structures: 
    2CM5, 2CM6

  • 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 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, and the University of Göttingen, 37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 38.47 kDa 
  • Atom Count: 2,397 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 332 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RABPHILIN-3A
A, B
166Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P47709 (Rattus norvegicus)
Explore P47709 
Go to UniProtKB:  P47709
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47709
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.268 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.195 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.069α = 90
b = 59.606β = 103.89
c = 66.385γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description