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 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1111/j.1742-4658.2005.04629.x
  • Primary Citation of Related Structures:  

  • 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, 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sarcoplasmic calcium-binding protein174Hediste diversicolorMutation(s): 0 
Find proteins for P04571 (Hediste diversicolor)
Explore P04571 
Go to UniProtKB:  P04571
Entity Groups  
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UniProt GroupP04571
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references