3NLA

NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, 40 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 40 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the binding of a globular antifreeze protein to ice.

Jia, Z.DeLuca, C.I.Chao, H.Davies, P.L.

(1996) Nature 384: 285-288

  • DOI: 10.1038/384285a0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antifreeze proteins (AFPs) have the unique ability to adsorb to ice and inhibit its growth. Many organisms ranging from fish to bacteria use AFPs to retard freezing or lessen the damage incurred upon freezing and thawing. The ice-binding mechanism of ...

    Antifreeze proteins (AFPs) have the unique ability to adsorb to ice and inhibit its growth. Many organisms ranging from fish to bacteria use AFPs to retard freezing or lessen the damage incurred upon freezing and thawing. The ice-binding mechanism of the long linear alpha-helical type I AFPs has been attributed to their regularly spaced polar residues matching the ice lattice along a pyramidal plane. In contrast, it is not known how globular antifreeze proteins such as type III AFP that lack repeating ice-binding residues bind to ice. Here we report the 1.25 A crystal structure of recombinant type III AFP (QAE isoform) from eel pout (Macrozoarces americanus), which reveals a remarkably flat amphipathic ice-binding site where five hydrogen-bonding atoms match two ranks of oxygens on the [1010] ice prism plane in the <0001> direction, giving high ice-binding affinity and specificity. This binding site, substantiated by the structures and properties of several ice-binding site mutants, suggests that the AFP occupies a niche in the ice surface in which it covers the basal plane while binding to the prism face.


    Related Citations: 
    • Refined Solution Structure of Type III Antifreeze Protein: Hydrophobic Groups May be Involved in the Energetics of the Protein-Ice Interaction
      Sonnichsen, F.D.,Deluca, C.I.,Davies, P.L.,Sykes, B.D.
      (1996) Structure 4: 1325
    • Antifreeze Peptide Heterogeneity in an Antarctic Eel Pout Includes an Unusually Large Major Variant Comprised of Two 7 kDa Type III Afps Linked in Tandem
      Wang, X.,Devries, A.L.,Cheng, C.H.
      (1995) Biochim.Biophys.Acta 1247: 163
    • Structural Basis for the Binding of a Globular Antifreeze Protein to Ice
      Jia, Z.,Deluca, C.I.,Chao, H.,Davies, P.L.
      (1996) Nature 384: 285


    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario, Canada. jia@crystal.biochem.queensu.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIFREEZE PROTEIN RD3 TYPE III
A
74Lycodichthys dearborniMutation(s): 0 
Find proteins for P35753 (Lycodichthys dearborni)
Go to UniProtKB:  P35753
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 40 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
  • Olderado: 3NLA Olderado
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-23
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance