4KE2

Crystal structure of the hyperactive Type I antifreeze from winter flounder


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.

Sun, T.Lin, F.H.Campbell, R.L.Allingham, J.S.Davies, P.L.

(2014) Science 343: 795-798

  • DOI: 10.1126/science.1247407

  • PubMed Abstract: 
  • When polypeptide chains fold into a protein, hydrophobic groups are compacted in the center with exclusion of water. We report the crystal structure of an alanine-rich antifreeze protein that retains ~400 waters in its core. The putative ice-binding ...

    When polypeptide chains fold into a protein, hydrophobic groups are compacted in the center with exclusion of water. We report the crystal structure of an alanine-rich antifreeze protein that retains ~400 waters in its core. The putative ice-binding residues of this dimeric, four-helix bundle protein point inwards and coordinate the interior waters into two intersecting polypentagonal networks. The bundle makes minimal protein contacts between helices, but is stabilized by anchoring to the semi-clathrate water monolayers through backbone carbonyl groups in the protein interior. The ordered waters extend outwards to the protein surface and likely are involved in ice binding. This protein fold supports both the anchored-clathrate water mechanism of antifreeze protein adsorption to ice and the water-expulsion mechanism of protein folding.


    Related Citations: 
    • Hyperactive antifreeze protein from fish contains multiple ice-binding sites.
      Graham, L.A.,Marshall, C.B.,Lin, F.H.,Campbell, R.L.,Davies, P.L.
      (2008) Biochemistry 47: 2051
    • Hyperactive antifreeze protein from winter flounder is a very long rod-like dimer of alpha-helices.
      Marshall, C.B.,Chakrabartty, A.,Davies, P.L.
      (2005) J.Biol.Chem. 280: 17920


    Organizational Affiliation

    Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type I hyperactive antifreeze protein
A, B, C
196Pseudopleuronectes americanusMutation(s): 0 
Find proteins for B1P0S1 (Pseudopleuronectes americanus)
Go to UniProtKB:  B1P0S1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.820α = 90.00
b = 48.140β = 91.87
c = 182.540γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
autoSHARPphasing
XSCALEdata scaling
SHARPphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references