7BWY

Crystal structure of ice-binding protein from an Antarctic ascomycete, Antarctomyces psychrotrophicus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes.

Yamauchi, A.Arai, T.Kondo, H.Sasaki, Y.C.Tsuda, S.

(2020) Biomolecules 10

  • DOI: https://doi.org/10.3390/biom10050759
  • Primary Citation of Related Structures:  
    7BWX, 7BWY

  • PubMed Abstract: 

    Many microbes that survive in cold environments are known to secrete ice-binding proteins (IBPs). The structure-function relationship of these proteins remains unclear. A microbial IBP denoted Anp IBP was recently isolated from a cold-adapted fungus, Antarctomyces psychrotrophicus . The present study identified an orbital illumination (prism ring) on a globular single ice crystal when soaked in a solution of fluorescent Anp IBP, suggesting that Anp IBP binds to specific water molecules located in the ice prism planes. In order to examine this unique ice-binding mechanism, we carried out X-ray structural analysis and mutational experiments. It appeared that Anp IBP is made of 6-ladder β-helices with a triangular cross section that accompanies an "ice-like" water network on the ice-binding site. The network, however, does not exist in a defective mutant. Anp IBP has a row of four unique hollows on the IBS, where the distance between the hollows (14.7 Å) is complementary to the oxygen atom spacing of the prism ring. These results suggest the structure of Anp IBP is fine-tuned to merge with the ice-water interface of an ice crystal through its polygonal water network and is then bound to a specific set of water molecules constructing the prism ring to effectively halt the growth of ice.


  • Organizational Affiliation

    Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ice-binding protein isoform1a
A, B, C
222Antarctomyces psychrotrophicusMutation(s): 2 
Gene Names: ibp
UniProt
Find proteins for A0A2Z6DSM4 (Antarctomyces psychrotrophicus)
Explore A0A2Z6DSM4 
Go to UniProtKB:  A0A2Z6DSM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2Z6DSM4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.311α = 90
b = 92.311β = 90
c = 222.669γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H02529
Japan Society for the Promotion of Science (JSPS)Japan19K22989

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description