8V66 | pdb_00008v66

Nanorana parkeri saxiphilin:GTX5 (co-crystal)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural basis for saxitoxin congener binding and neutralization by anuran saxiphilins.

Zakrzewska, S.Nixon, S.A.Chen, Z.Hajare, H.S.Park, E.R.Mulcahy, J.V.Arlinghaus, K.M.Neu, E.Konovalov, K.Provasi, D.Leighfield, T.A.Filizola, M.Du Bois, J.Minor Jr., D.L.

(2025) Nat Commun 16: 3885-3885

  • DOI: https://doi.org/10.1038/s41467-025-58903-2
  • Primary Citation of Related Structures:  
    8V65, 8V66, 8V67, 8V68, 8V69

  • PubMed Abstract: 

    Dinoflagellates and cyanobacteria produce saxitoxin (STX) and ~50 congeners that disrupt bioelectrical signals by blocking voltage-gated sodium channels (Na V s). Consuming seafood carrying these toxins causes paralytic shellfish poisoning (PSP). Although Na V s and anuran STX binding proteins (saxiphilins, Sxphs) use convergent STX binding modes, the structural basis for STX congener recognition is unknown. Here, we show that American bullfrog (Rana catesbeiana) RcSxph and High Himalaya frog (Nanorana parkeri) NpSxph sequester STX congeners using a 'lock and key' mode shared with STX. Importantly, functional studies demonstrate that Sxph 'toxin sponges' reverse Na V block by multiple STX congeners and detect these toxins in a radioligand binding assay (RBA) used for environmental testing. Together, our study establishes how Sxphs sequester select neurotoxins and uncover STX congener-specific interactions distinct from Na V s. These findings expand understanding of toxin sponge action and provide a foundation for strategies to monitor and mitigate the harmful effects of STX congeners.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Saxiphilin854Nanorana parkeriMutation(s): 0 
Gene Names: XM_018555331.1
UniProt
Find proteins for A0A9X9ZA84 (Nanorana parkeri)
Explore A0A9X9ZA84 
Go to UniProtKB:  A0A9X9ZA84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X9ZA84
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YGZ (Subject of Investigation/LOI)
Query on YGZ

Download Ideal Coordinates CCD File 
C [auth A]({[(3aS,4R,7S,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methoxy}carbonyl)sulfamic acid
C10 H17 N7 O7 S
JKKCSFJSULZNDN-HGRQIUPRSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
B [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 229.156α = 90
b = 229.156β = 90
c = 67.505γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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: 2025-05-07
    Type: Initial release