5PAL

CRYSTAL STRUCTURE OF THE UNIQUE PARVALBUMIN COMPONENT FROM MUSCLE OF THE LEOPARD SHARK (TRIAKIS SEMIFASCIATA). THE FIRST X-RAY STUDY OF AN ALPHA-PARVALBUMIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Observed: 0.173 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin.

Roquet, F.Declercq, J.P.Tinant, B.Rambaud, J.Parello, J.

(1992) J Mol Biol 223: 705-720

  • DOI: 10.1016/0022-2836(92)90985-s
  • Primary Citation of Related Structures:  
    5PAL

  • PubMed Abstract: 
  • The three-dimensional structure of parvalbumin from leopard shark (Triakis semifasciata) with 109 amino acid residues (alpha-series) is described at 1.54 A resolution. Crystals were grown at 20 degrees C from 2.9 M-potassium/sodium phosphate solutions at pH 5 ...

    The three-dimensional structure of parvalbumin from leopard shark (Triakis semifasciata) with 109 amino acid residues (alpha-series) is described at 1.54 A resolution. Crystals were grown at 20 degrees C from 2.9 M-potassium/sodium phosphate solutions at pH 5.6. The space group is P3(1)21 and unit cell dimensions are a = b = 32.12 A and c = 149.0 A. The structure has been solved by the molecular replacement method using pike 4.10 parvalbumin as a model. The final structure refinement resulted in an R-factor of 17.3% for 11,363 independent reflections at 1.54 A resolution. The shark parvalbumin shows the main features of all parvalbumins: the folding of the chain including six alpha-helices, the salt bridge between Arg75 and Glu81, and the hydrophobic core. Compared to the structure of beta-parvalbumins from pike and carp, one main difference is observed: the chain is one residue longer and this additional residue, which extends the F helix, is involved through its C-terminal carboxylate group in a network of electrostatic contacts with two basic residues, His31 in the B helix and Lys36 in the BC segment. Furthermore, hydrogen bonds exist between the side-chains of Gln108 (F helix) and Tyr26 (B helix). There is therefore a "locking" of the tertiary structure through contacts between two sequentially distant regions in the protein and this is likely to contribute to making the stability of an alpha-parvalbumin higher in comparison to that of a beta-parvalbumin. The lengthening of the C-terminal F helix by one residue appears to be a major feature of alpha-parvalbumins in general, owing to the homologies of the amino acid sequences. Besides the lengthening of the C-terminal helix, the classification of the leopard shark parvalbumin in the alpha-series rests upon the observation of Lys13, Leu32, Glu61 and Val66. As this is the first crystal structure description of a parvalbumin from the alpha-phylogenetic lineage, it was hoped that it would clearly determine the presence or absence of a third cation binding site in parvalbumins belonging to the alpha-lineage. In beta-pike pI 4.10 parvalbumin, Asp61 participates as a direct ligand of a third site, the satellite of the CD site. In shark parvalbumin, as in nearly all alpha-parvalbumins, one finds Glu at position 61. Unfortunately, the conformation of the polar head of Glu61 cannot be inferred from the X-ray data.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Ionic Interactions with Parvalbumins. Crystal Structure Determination of Pike 4(Dot)10 Parvalbumin in Four Different Ionic Environments
      Declercq, J.-P., Tinant, B., Parello, J., Rambaud, J.
      (1991) J Mol Biol 220: 1017
    • Crystal Structure Determination and Refinement of Pike 4.10 Parvalbumin (Minor Component from Esox Lucius)
      Declercq, J.-P., Tinant, B., Parello, J., Etienne, G., Huber, H.
      (1988) J Mol Biol 202: 349

    Organizational Affiliation

    Laboratoire de Chimie-Physique et de Cristallographie, Université Catholique de Louvain, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PARVALBUMINA109Triakis semifasciataMutation(s): 0 
Find proteins for P30563 (Triakis semifasciata)
Explore P30563 
Go to UniProtKB:  P30563
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Observed: 0.173 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.12α = 90
b = 32.12β = 90
c = 149γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
EREFrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations, Other