1RJV

Solution Structure of Human alpha-Parvalbumin refined with a paramagnetism-based strategy


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 19 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Paramagnetism-Based Refinement Strategy for the Solution Structure of Human alpha-Parvalbumin.

Baig, I.Bertini, I.Del Bianco, C.Gupta, Y.K.Lee, Y.M.Luchinat, C.Quattrone, A.

(2004) Biochemistry 43: 5562-5573

  • DOI: https://doi.org/10.1021/bi035879k
  • Primary Citation of Related Structures:  
    1RJV, 1RK9

  • PubMed Abstract: 

    In the frame of a research aimed at the detailed structural characterization of human calcium-binding proteins of the EF-hand family, the solution structure of human alpha-parvalbumin has been solved by NMR and refined with the help of substitution of the Ca(2+) ion in the EF site with the paramagnetic Dy(3+) ion. A simple (1)H-(15)N HSQC spectrum allowed the NH assignments based on the properties of Dy(3+). This allowed us to exploit pseudocontact shifts and residual dipolar couplings for solution structure refinement. The backbone and heavy atom RMSD are 0.55 +/- 0.08 and 1.02 +/- 0.08 A, respectively, and decrease to 0.39 +/- 0.05 and 0.90 +/- 0.06 A upon refinement with paramagnetism-based restraints. The RMSD for the metal itself in the EF site in the refined structure is 0.26 +/- 0.12 A. Backbone NH R(1), R(2), and NOE measured at two temperatures show the protein to be relatively rigid. The NH orientations are well determined by the paramagnetism-based restraints. This allows us to detect small but significant local structural differences with the orthologue protein from rat, whose X-ray structure is available at 2.0 A resolution. All differences are related to local changes in the amino acidic composition.


  • Organizational Affiliation

    Magnetic Resonance Centre and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Parvalbumin alpha110Homo sapiensMutation(s): 0 
Gene Names: PVALB
UniProt & NIH Common Fund Data Resources
Find proteins for P20472 (Homo sapiens)
Explore P20472 
Go to UniProtKB:  P20472
GTEx:  ENSG00000100362 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20472
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 19 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-25
    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: 2022-03-02
    Changes: Data collection, Database references, Derived calculations