Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 40 
  • Selection Criteria: AVERAGE 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


NMR analysis of type III antifreeze protein intramolecular dimer. Structural basis for enhanced activity.

Miura, K.Ohgiya, S.Hoshino, T.Nemoto, N.Suetake, T.Miura, A.Spyracopoulos, L.Kondo, H.Tsuda, S.

(2001) J Biol Chem 276: 1304-1310

  • DOI: https://doi.org/10.1074/jbc.M007902200
  • Primary Citation of Related Structures:  
    1C89, 1C8A

  • PubMed Abstract: 

    The structure of a new antifreeze protein (AFP) variant, RD3, from antarctic eel pout (Rhigophila dearborni) with enhanced activity has been determined for the first time by nuclear magnetic resonance spectroscopy. RD3 comprises a unique translational topology of two homologous type III AFP globular domains, each containing one flat, ice binding plane. The ice binding plane of the N domain is located approximately 3.5 A "behind" that of the C domain. The two ice binding planes are located laterally with an angle of 32 +/- 12 degrees between the planes. These results suggest that the C domain plane of RD3 binds first to the ice [1010] prism plane in the <0001> direction, which induces successive ice binding of the N domain in the <0101> direction. This manner of ice binding caused by the unique structural topology of RD3 is thought to be crucial for the significant enhancement of antifreeze activity, especially at low AFP concentrations.

  • Organizational Affiliation

    Bioscience and Chemistry Division, Hokkaido National Industrial Research Institute, 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIFREEZE PROTEIN TYPE III134Pachycara brachycephalumMutation(s): 0 
Find proteins for P35753 (Lycodichthys dearborni)
Explore P35753 
Go to UniProtKB:  P35753
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35753
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 40 
  • Selection Criteria: AVERAGE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-28
    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: 2022-02-16
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection