2CHD

Crystal structure of the C2A domain of Rabphilin-3A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the C2A Domain of Rabphilin-3A.

Biadene, M.Montaville, P.Sheldrick, G.M.Becker, S.

(2006) Acta Crystallogr.,Sect.D 62: 793

  • DOI: 10.1107/S0907444906017537

  • PubMed Abstract: 
  • Rabphilin-3A is a neuronal protein containing a C2-domain tandem. To date, only the structure of the C2B domain has been solved. The crystal structure of the Ca2+-free C2A domain has been solved by molecular replacement and refined to 1.92 A resoluti ...

    Rabphilin-3A is a neuronal protein containing a C2-domain tandem. To date, only the structure of the C2B domain has been solved. The crystal structure of the Ca2+-free C2A domain has been solved by molecular replacement and refined to 1.92 A resolution. It adopts the classical C2-domain fold consisting of an eight-stranded antiparallel beta-sandwich with type I topology. In agreement with its Ca2+-dependent negatively charged membrane-binding properties, this C2 domain contains all the conserved acidic residues responsible for calcium binding. However, the replacement of a conserved aspartic acid residue by glutamic acid allows formation of an additional strong hydrogen bond, resulting in increased rigidity of calcium-binding loop 1. The electrostatic surface of the C2A domain consists of a large positively charged belt surrounded by two negatively charged patches located at both tips of the domain. In comparison, the structurally very similar C2A domain of synaptotagmin I has a highly acidic electrostatic surface, suggesting completely unrelated functions for these two C2A domains.


    Organizational Affiliation

    Department of Structural Chemistry, University of Göttingen, Tammanstrasse 4, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RABPHILIN-3A
A
142Rattus norvegicusMutation(s): 0 
Gene Names: Rph3a
Find proteins for P47709 (Rattus norvegicus)
Go to UniProtKB:  P47709
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.870α = 90.00
b = 39.160β = 90.00
c = 88.850γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2018-05-30
    Type: Data collection