2KSZ | pdb_00002ksz

The solution structure of the Magnesium bound soybean calmodulin isoform 4 N-domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest RDC energy 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The solution structure of the Mg2+ form of soybean calmodulin isoform 4 reveals unique features of plant calmodulins in resting cells.

Huang, H.Ishida, H.Vogel, H.J.

(2010) Protein Sci 19: 475-485

  • DOI: https://doi.org/10.1002/pro.325
  • Primary Citation Related Structures: 
    2KSZ

  • PubMed Abstract: 

    Soybean calmodulin isoform 4 (sCaM4) is a plant calcium-binding protein, regulating cellular responses to the second messenger Ca(2+). We have found that the metal ion free (apo-) form of sCaM4 possesses a half unfolded structure, with the N-terminal domain unfolded and the C-terminal domain folded. This result was unexpected as the apo-forms of both soybean calmodulin isoform 1 (sCaM1) and mammalian CaM (mCaM) are fully folded. Because of the fact that free Mg(2+) ions are always present at high concentrations in cells (0.5-2 mM), we suggest that Mg(2+) should be bound to sCaM4 in nonactivated cells. CD studies revealed that in the presence of Mg(2+) the initially unfolded N-terminal domain of sCaM4 folds into an alpha-helix-rich structure, similar to the Ca(2+) form. We have used the NMR backbone residual dipolar coupling restraints (1)D(NH), (1)D(C alpha H alpha), and (1)D(C'C alpha) to determine the solution structure of the N-terminal domain of Mg(2+)-sCaM4 (Mg(2+)-sCaM4-NT). Compared with the known structure of Ca(2+)-sCaM4, the structure of the Mg(2+)-sCaM4-NT does not fully open the hydrophobic pocket, which was further confirmed by the use of the fluorescent probe ANS. Tryptophan fluorescence experiments were used to study the interactions between Mg(2+)-sCaM4 and CaM-binding peptides derived from smooth muscle myosin light chain kinase and plant glutamate decarboxylase. These results suggest that Mg(2+)-sCaM4 does not bind to Ca(2+)-CaM target peptides and therefore is functionally similar to apo-mCaM. The Mg(2+)- and apo-structures of the sCaM4-NT provide unique insights into the structure and function of some plant calmodulins in resting cells.


  • Organizational Affiliation
    • Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

Macromolecule Content 

  • Total Structure Weight: 8.48 kDa 
  • Atom Count: 592 
  • Modeled Residue Count: 76 
  • Deposited Residue Count: 76 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein76Glycine maxMutation(s): 0 
Gene Names: SCaM-4
UniProt
Find proteins for Q39890 (Glycine max)
Explore Q39890 
Go to UniProtKB:  Q39890
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39890
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest RDC energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-12-10
    Changes: Structure summary
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations