9Y91 | pdb_00009y91

Nanorana parkeri saxiphilin:STX-C13-NBz (co-crystal)

• PDB DOI: https://doi.org/10.2210/pdb9Y91/pdb

• Classification: ANTITOXIN
• Organism(s): Nanorana parkeri
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-09-12 Released: 2026-05-27 
• Deposition Author(s): Zakrzewska, S., Minor, D.L.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Saxiphilin is a broad-spectrum toxin sponge for C13-modified saxitoxins.

Zakrzewska, S., Chen, Z., Park, E.R., Bhaskar, R.G., Bedell, T.A., Du Bois, J., Minor Jr., D.L.

(2026) Structure 

• PubMed: 42309055 
• DOI: https://doi.org/10.1016/j.str.2026.05.008
• Primary Citation Related Structures: 
  9Y91, 9Y92, 9YAR, 9YAS, 9YAT, 9YAV, 9YBD, 9YBE, 9YBF


• PubMed Abstract: 
  

  Saxitoxin (STX) and its congeners (paralytic shellfish toxins, PSTs) are among the most potent small-molecule toxins. PSTs are produced by harmful algal blooms and derive toxicity by disrupting voltage-gated sodium channel (Na _V ) bioelectrical signaling. Understanding how PST structural variation affects target binding is crucial for toxin countermeasure development and exploitation of PSTs as drug development leads. Frog and toad saxiphilins (Sxphs) are soluble, high-affinity STX toxin sponges that offer a powerful platform to define PST-protein interactions. Here, we show that American bullfrog (Rana catesbeiana) RcSxph and High Himalaya frog (Nanorana parkeri) NpSxph bind a broad set of C13-modified STX congeners. High-resolution structures unveil "compact" and "open" C13-aryl congener binding modes that depend on the RcSxph Tyr558 environment, highlighting a remarkable adaptability of Sxphs to bind STX analogs and unexpected toxin conformational plasticity. These findings have implications for understanding PST interactions with biological targets and informing design of Na _V probes and modulators.

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Organizational Affiliation: 
• Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95.3 kDa 
• Atom Count: 6,826 
• Modeled Residue Count: 821 
• Deposited Residue Count: 854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saxiphilin	A	854	Nanorana parkeri	Mutation(s): 0  Gene Names: XM_018555331.1
UniProt
Find proteins for A0A9X9ZA84 (Nanorana parkeri) Explore A0A9X9ZA84  Go to UniProtKB:  A0A9X9ZA84

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CTW (Subject of Investigation/LOI)	C [auth A]	N-{[(2Z,3aS,4S,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl}benzamide C16 H21 N7 O3 ACZTTYAVNQAOMZ-MMPTUQATSA-N
1PE	B [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 228.982	α = 90
b = 228.982	β = 90
c = 67.487	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Zakrzewska, S., Minor, D.L.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	HDTRA-1-19-1-0040
Department of Defense (DOD, United States)	United States	HDTRA-1-21-1-10011
Department of Defense (DOD, United States)	United States	HDTRA-1-23-1-0026

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release
  
• Version 1.1: 2026-07-01
  Changes: Database references
• Version 1.2: 2026-07-08
  Changes: Database references