1K94

Crystal structure of des(1-52)grancalcin with bound calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Ca(2+)-loaded human grancalcin.

Jia, J.Borregaard, N.Lollike, K.Cygler, M.

(2001) Acta Crystallogr.,Sect.D 57: 1843-1849

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Grancalcin is a cytosolic Ca(2+)-binding protein originally identified in human neutrophils. It belongs to a new class of EF-hand proteins, called PEF proteins, which contain five EF-hand motifs. At the N-terminus of grancalcin there is a approximate ...

    Grancalcin is a cytosolic Ca(2+)-binding protein originally identified in human neutrophils. It belongs to a new class of EF-hand proteins, called PEF proteins, which contain five EF-hand motifs. At the N-terminus of grancalcin there is a approximately 50 residue-long segment rich in glycines and prolines. The fifth EF-hand, unpaired within the monomer, provides a means for dimerization through pairing with its counterpart in a second molecule. The structure of full-length grancalcin in the apo form and with one EF3 within the dimer occupied by a Ca(2+) ion have been determined. Although the N-terminal segment was present in the molecule, this part was disordered in the crystals. Here, the structure of a truncated form of grancalcin, which is lacking 52 N-terminal residues, in the presence and absence of Ca(2+) is presented. In the Ca(2+)-bound form the ions are found in the EF1 and EF3 hands. Binding of Ca(2+) to these two EF hands produces only minor conformational changes, mostly within the EF1 Ca(2+)-binding loop. This observation supports the hypothesis, formulated on the basis of the structure of a homologous protein ALG-2 which shows significant differences in the orientation of EF4 and EF5 compared with grancalcin, that calcium is a necessary factor but not sufficient alone for inducing a significant conformational change in PEF proteins.


    Related Citations: 
    • Crystallizaiton and preliminary X-ray analysis of human grancalcin, a novel Ca2+-binding protein in leukocytes
      Han, Q.,Jia, J.,Li, Y.,Lollike, K.,Cygler, M.
      (2000) Acta Crystallogr.,Sect.D 56: 772
    • Crystal structure of human grancalcin, a member of the Penta-EF-Hand Protein family
      Jia, J.,Han, Q.,Borregaard, N.,Lollike, K.,Cygler, M.
      (2000) J.Mol.Biol. 300: 1271


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GRANCALCIN
A, B
165Homo sapiensMutation(s): 0 
Gene Names: GCA (GCL)
Find proteins for P28676 (Homo sapiens)
Go to Gene View: GCA
Go to UniProtKB:  P28676
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: 1.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.120α = 90.00
b = 71.130β = 90.00
c = 77.570γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance