Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.197 

Starting Model: experimental
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Quantitative and qualitative analysis of type III antifreeze protein structure and function.

Graether, S.P.DeLuca, C.I.Baardsnes, J.Hill, G.A.Davies, P.L.Jia, Z.

(1999) J Biol Chem 274: 11842-11847

  • DOI: https://doi.org/10.1074/jbc.274.17.11842
  • Primary Citation of Related Structures:  
    1B7I, 1B7J, 1B7K, 1EKL, 1JAB, 1MSJ, 2AME, 2JIA, 2MSJ, 2SPG, 3AME, 4AME, 6AME, 7AME, 8AME, 8MSI, 9AME, 9MSI

  • PubMed Abstract: 

    Some cold water marine fishes avoid cellular damage because of freezing by expressing antifreeze proteins (AFPs) that bind to ice and inhibit its growth; one such protein is the globular type III AFP from eel pout. Despite several studies, the mechanism of ice binding remains unclear because of the difficulty in modeling the AFP-ice interaction. To further explore the mechanism, we have determined the x-ray crystallographic structure of 10 type III AFP mutants and combined that information with 7 previously determined structures to mainly analyze specific AFP-ice interactions such as hydrogen bonds. Quantitative assessment of binding was performed using a neural network with properties of the structure as input and predicted antifreeze activity as output. Using the cross-validation method, a correlation coefficient of 0.60 was obtained between measured and predicted activity, indicating successful learning and good predictive power. A large loss in the predictive power of the neural network occurred after properties related to the hydrophobic surface were left out, suggesting that van der Waal's interactions make a significant contribution to ice binding. By combining the analysis of the neural network with antifreeze activity and x-ray crystallographic structures of the mutants, we extend the existing ice-binding model to a two-step process: 1) probing of the surface for the correct ice-binding plane by hydrogen-bonding side chains and 2) attractive van der Waal's interactions between the other residues of the ice-binding surface and the ice, which increases the strength of the protein-ice interaction.

  • Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario, K7L 3N6 Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (ANTIFREEZE PROTEIN TYPE III)66Zoarces americanusMutation(s): 3 
Find proteins for P19614 (Zoarces americanus)
Explore P19614 
Go to UniProtKB:  P19614
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19614
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.715α = 90
b = 39.125β = 90
c = 46.616γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-29
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description