6O0F | pdb_00006o0f

Saxiphilin:STX complex, co-crystal

• PDB DOI: https://doi.org/10.2210/pdb6O0F/pdb

• Classification: ANTITOXIN
• Organism(s): Aquarana catesbeiana
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-02-16 Released: 2019-07-10 
• Deposition Author(s): Yen, T.J., Lolicato, M., Minor, D.L.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Structure of the saxiphilin:saxitoxin (STX) complex reveals a convergent molecular recognition strategy for paralytic toxins.

Yen, T.J., Lolicato, M., Thomas-Tran, R., Du Bois, J., Minor Jr., D.L.

(2019) Sci Adv 5: eaax2650-eaax2650

• PubMed: 31223657 
• DOI: https://doi.org/10.1126/sciadv.aax2650
• Primary Citation Related Structures: 
  6O0D, 6O0E, 6O0F


• PubMed Abstract: 
  

  Dinoflagelates and cyanobacteria produce saxitoxin (STX), a lethal bis-guanidinium neurotoxin causing paralytic shellfish poisoning. A number of metazoans have soluble STX-binding proteins that may prevent STX intoxication. However, their STX molecular recognition mechanisms remain unknown. Here, we present structures of saxiphilin (Sxph), a bullfrog high-affinity STX-binding protein, alone and bound to STX. The structures reveal a novel high-affinity STX-binding site built from a "proto-pocket" on a transferrin scaffold that also bears thyroglobulin domain protease inhibitor repeats. Comparison of Sxph and voltage-gated sodium channel STX-binding sites reveals a convergent toxin recognition strategy comprising a largely rigid binding site where acidic side chains and a cation-π interaction engage STX. These studies reveal molecular rules for STX recognition, outline how a toxin-binding site can be built on a naïve scaffold, and open a path to developing protein sensors for environmental STX monitoring and new biologics for STX intoxication mitigation.

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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.
Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
California Institute for Quantitative Biomedical Research, 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 189.06 kDa 
• Atom Count: 12,816 
• Modeled Residue Count: 1,628 
• Deposited Residue Count: 1,706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saxiphilin	A, B	853	Aquarana catesbeiana	Mutation(s): 0
UniProt
Find proteins for P31226 (Aquarana catesbeiana) Explore P31226  Go to UniProtKB:  P31226

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9SL	C [auth A], D [auth B]	[(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate C10 H17 N7 O4 RPQXVSUAYFXFJA-HGRQIUPRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.563	α = 90
b = 111.656	β = 90
c = 254.624	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Yen, T.J., Lolicato, M., Minor, D.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01-HL080050
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM117263-01A1

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary