4UR4

Structure of the type III fish antifreeze protein from Zoarces viviparus ZvAFP13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 

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This is version 1.3 of the entry. See complete history


Literature

Purification, Crystal Structure Determination and Functional Characterization of Type III Antifreeze Proteins from the European Eelpout Zoarces Viviparus.

Wilkens, C.Poulsen, J.N.Ramlov, H.Lo Leggio, L.

(2014) Cryobiology 69: 163

  • DOI: https://doi.org/10.1016/j.cryobiol.2014.07.003
  • Primary Citation of Related Structures:  
    4UR4, 4UR6

  • PubMed Abstract: 

    Antifreeze proteins (AFPs) are essential components of many organisms adaptation to cold temperatures. Fish type III AFPs are divided into two groups, SP isoforms being much less active than QAE1 isoforms. Two type III AFPs from Zoarces viviparus, a QAE1 (ZvAFP13) and an SP (ZvAFP6) isoform, are here characterized and their crystal structures determined. We conclude that the higher activity of the QAE1 isoforms cannot be attributed to single residues, but rather a combination of structural effects. Furthermore both ZvAFP6 and ZvAFP13 crystal structures have water molecules around T18 equivalent to the tetrahedral-like waters previously identified in a neutron crystal structure. Interestingly, ZvAFP6 forms dimers in the crystal, with a significant dimer interface. The presence of ZvAFP6 dimers was confirmed in solution by native electrophoresis and gel filtration. To our knowledge this is the first report of dimerization of AFP type III proteins.


  • Organizational Affiliation

    Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark. Electronic address: cwil@bio.dtu.dk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIFREEZE PROTEIN 1367Zoarces viviparusMutation(s): 0 
UniProt
Find proteins for A3EYI7 (Zoarces viviparus)
Explore A3EYI7 
Go to UniProtKB:  A3EYI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3EYI7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.26α = 90
b = 39.69β = 90
c = 44.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description