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 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 D Biol Crystallogr 62: 793

  • DOI: https://doi.org/10.1107/S0907444906017537
  • Primary Citation of Related Structures:  
    2CHD

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RABPHILIN-3A142Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.87α = 90
b = 39.16β = 90
c = 88.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-05-30
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description