1Q80

Solution structure and dynamics of Nereis sarcoplasmic calcium binding protein


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 17 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure and internal dynamics of NSCP, a compact calcium-binding protein.

Rabah, G.Popescu, R.Cox, J.A.Engelborghs, Y.Craescu, C.T.

(2005) Febs J. 272: 2022-2036

  • DOI: 10.1111/j.1742-4658.2005.04629.x

  • PubMed Abstract: 
  • The solution structure of Nereis diversicolor sarcoplasmic calcium-binding protein (NSCP) in the calcium-bound form was determined by NMR spectroscopy, distance geometry and simulated annealing. Based on 1859 NOE restraints and 262 angular restraints ...

    The solution structure of Nereis diversicolor sarcoplasmic calcium-binding protein (NSCP) in the calcium-bound form was determined by NMR spectroscopy, distance geometry and simulated annealing. Based on 1859 NOE restraints and 262 angular restraints, 17 structures were generated with a rmsd of 0.87 A from the mean structure. The solution structure, which is highly similar to the structure obtained by X-ray crystallography, includes two open EF-hand domains, which are in close contact through their hydrophobic surfaces. The internal dynamics of the protein backbone were determined by studying amide hydrogen/deuterium exchange rates and 15N nuclear relaxation. The two methods revealed a highly compact and rigid structure, with greatly restricted mobility at the two termini. For most of the amide protons, the free energy of exchange-compatible structural opening is similar to the free energy of structural stability, suggesting that isotope exchange of these protons takes place through global unfolding of the protein. Enhanced conformational flexibility was noted in the unoccupied Ca2+-binding site II, as well as the neighbouring helices. Analysis of the experimental nuclear relaxation and the molecular dynamics simulations give very similar profiles for the backbone generalized order parameter (S2), a parameter related to the amplitude of fast (picosecond to nanosecond) movements of N(H)-H vectors. We also noted a significant correlation between this parameter, the exchange rate, and the crystallographic B factor along the sequence.


    Related Citations: 
    • 1H and 15N Resonance Assignment of the Calcium-bound Form of the Nereis Diversicolor Sarcoplasmic Ca(2+)-binding Protein
      Craescu, C.T.,Precheur, B.,van Riel, A.,Sakamoto, H.,Cox, J.A.,Engelborghs, Y.
      (1998) J.Biomol.NMR 12: 565


    Organizational Affiliation

    INSERM & Institut Curie, Centre Universitaire, Orsay, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sarcoplasmic calcium-binding protein
A
174Hediste diversicolor
Find proteins for P04571 (Hediste diversicolor)
Go to UniProtKB:  P04571
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 17 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the least restraint violations 
  • Olderado: 1Q80 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance