8D6Q

Rana catesbeiana saxiphilin mutant - Y558I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

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

Definition of a saxitoxin (STX) binding code enables discovery and characterization of the anuran saxiphilin family.

Chen, Z.Zakrzewska, S.Hajare, H.S.Alvarez-Buylla, A.Abderemane-Ali, F.Bogan, M.Ramirez, D.O'Connell, L.A.Du Bois, J.Minor Jr., D.L.

(2022) Proc Natl Acad Sci U S A 119: e2210114119-e2210114119

  • DOI: https://doi.org/10.1073/pnas.2210114119
  • Primary Citation of Related Structures:  
    8D6G, 8D6M, 8D6O, 8D6P, 8D6Q, 8D6S, 8D6T, 8D6U

  • PubMed Abstract: 

    American bullfrog ( Rana castesbeiana ) saxiphilin ( Rc Sxph) is a high-affinity "toxin sponge" protein thought to prevent intoxication by saxitoxin (STX), a lethal bis-guanidinium neurotoxin that causes paralytic shellfish poisoning (PSP) by blocking voltage-gated sodium channels (Na V s). How specific Rc Sxph interactions contribute to STX binding has not been defined and whether other organisms have similar proteins is unclear. Here, we use mutagenesis, ligand binding, and structural studies to define the energetic basis of Sxph:STX recognition. The resultant STX "recognition code" enabled engineering of Rc Sxph to improve its ability to rescue Na V s from STX and facilitated discovery of 10 new frog and toad Sxphs. Definition of the STX binding code and Sxph family expansion among diverse anurans separated by ∼140 My of evolution provides a molecular basis for understanding the roles of toxin sponge proteins in toxin resistance and for developing novel proteins to sense or neutralize STX and related PSP toxins.


  • Organizational Affiliation

    Cardiovascular Research Institute, University of California, San Francisco, CA 94158.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Saxiphilin
A, B
851Aquarana catesbeianaMutation(s): 1 
UniProt
Find proteins for P31226 (Aquarana catesbeiana)
Explore P31226 
Go to UniProtKB:  P31226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31226
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.394α = 90
b = 107.145β = 90
c = 254.785γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesHDTRA-1-19-1-0040
Department of Defense (DOD, United States)United StatesHDTRA-1-21-1-10011

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description