1C8A

NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 translationa ...

    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.


    Related Citations: 
    • Determination of the Solution Structure of the N-Domain Plus Linker of Antarctic Eel Pout Antifreeze Protein Rd3
      Miura, K., Ohgiya, S., Hoshino, T., Nemoto, N., Odaira, M., Nitta, K., Tsuda, S.
      (1999) J Biochem 126: 387
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ANTIFREEZE PROTEIN TYPE III)A134Pachycara brachycephalumMutation(s): 0 
Find proteins for P35753 (Lycodichthys dearborni)
Explore P35753 
Go to UniProtKB:  P35753
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGE 
  • OLDERADO: 1C8A Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2000-05-04 
  • Released Date: 2001-02-28 
  • Deposition Author(s): Miura, K., Tsuda, S.

Revision History 

  • 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