1HT9

DOMAIN SWAPPING EF-HANDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

An extended hydrophobic core induces EF-hand swapping.

Hakansson, M.Svensson, A.Fast, J.Linse, S.

(2001) Protein Sci 10: 927-933

  • DOI: 10.1110/ps.47501
  • Primary Citation of Related Structures:  
    1HT9

  • PubMed Abstract: 
  • The structure of calbindin D(9k) with two substitutions was determined by X-ray crystallography at 1.8-A resolution. Unlike wild-type calbindin D(9k), which is a monomeric protein with two EF-hands, the structure of the mutated calbindin D(9k) reveals an intertwined dimer ...

    The structure of calbindin D(9k) with two substitutions was determined by X-ray crystallography at 1.8-A resolution. Unlike wild-type calbindin D(9k), which is a monomeric protein with two EF-hands, the structure of the mutated calbindin D(9k) reveals an intertwined dimer. In the dimer, two EF-hands of the monomers have exchanged places, and thus a 3D domain-swapped dimer has been formed. EF-hand I of molecule A is packed toward EF-hand II of molecule B and vice versa. The formation of a hydrophobic cluster, in a region linking the EF-hands, promotes the conversion of monomers to 3D domain-swapped dimers. We propose a mechanism by which domain swapping takes place via the apo form of calbindin D(9k). Once formed, the calbindin D(9k) dimers are remarkably stable, as with even larger misfolded aggregates like amyloids. Thus calbindin D(9k) dimers cannot be converted to monomers by dilution. However, heating can be used for conversion, indicating high energy barriers separating monomers from dimers.


    Related Citations: 
    • Symmetric Stabilization of Bound Ca2+ Ions Through Hydrogen Bonding of Coordinating Water Molecules. Ca2+ Binding Abd Structural Stability of Calbindin D9K Mutants
      Fast, J., Muranyi, A., Gippert, G.P., Thulin, E., Evenas, J., Linse, S., Hakansson, M., Svensson, A.L.
      () To be published --: --

    Organizational Affiliation

    Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, S-221 00 Lund, Sweden. Maria.Hakansson@mbfys.lu.se



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CALBINDIN D9KA, B76Bos taurusMutation(s): 2 
Gene Names: S100GCALB3S100D
UniProt
Find proteins for P02633 (Bos taurus)
Explore P02633 
Go to UniProtKB:  P02633
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.605α = 90
b = 48.241β = 96.98
c = 41.53γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
AMoREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-07-21
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2021-10-27
    Changes: Database references