3E3R

Crystal structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family

Dong, H.Li, X.Lou, Z.Xu, X.Su, D.Zhou, X.Zhou, W.Bartlam, M.Rao, Z.

(2008) J.Mol.Biol. 383: 455-464

  • DOI: 10.1016/j.jmb.2008.08.048

  • PubMed Abstract: 
  • Calcyphosine is an EF-hand protein involved in both Ca(2+)-phosphatidylinositol and cyclic AMP signal cascades, as well as in other cellular functions. The crystal structure of Ca(2+)-loaded calcyphosine was determined up to 2.65 A resolution and rev ...

    Calcyphosine is an EF-hand protein involved in both Ca(2+)-phosphatidylinositol and cyclic AMP signal cascades, as well as in other cellular functions. The crystal structure of Ca(2+)-loaded calcyphosine was determined up to 2.65 A resolution and reveals a protein containing two pairs of Ca(2+)-binding EF-hand motifs. Calcyphosine shares a highly similar overall topology with calmodulin. However, there are striking differences between EF-hand 4, both N-terminal and C-terminal regions, and interdomain linkers. The C-terminal domain of calcyphosine possesses a large hydrophobic pocket in the presence of calcium ions that might be implicated in ligand binding, while its N-terminal hydrophobic pocket is almost shielded by an additional terminal helix. Calcyphosine is largely monomeric, regardless of the presence of Ca(2+). Differences in structure, oligomeric state in the presence and in the absence of Ca(2+), a highly conserved sequence with low similarity to other proteins, and phylogeny define a new EF-hand-containing family of calcyphosine proteins that extends from arthropods to humans.


    Organizational Affiliation

    Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calcyphosin
A, B
204Homo sapiensMutation(s): 0 
Gene Names: CAPS
Find proteins for Q13938 (Homo sapiens)
Go to Gene View: CAPS
Go to UniProtKB:  Q13938
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.593α = 90.00
b = 130.411β = 90.00
c = 46.199γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-08-07 
  • Released Date: 2008-08-26 
  • Deposition Author(s): Dong, H.

Revision History 

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance