6O0E

Saxiphilin:STX complex, soaking

  • Classification: ANTITOXIN
  • Organism(s): Lithobates catesbeianus
  • 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)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1126/sciadv.aax2650
  • Primary Citation of Related Structures:  
    6O0D, 6O0F, 6O0E

  • 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 ...

    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.


    Organizational Affiliation

    Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SaxiphilinA, B853Lithobates catesbeianusMutation(s): 0 
UniProt
Find proteins for P31226 (Lithobates catesbeianus)
Explore P31226 
Go to UniProtKB:  P31226
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9SL (Subject of Investigation/LOI)
Query on 9SL

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9SL Binding MOAD:  6O0E Kd: 0.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.379α = 90
b = 110.759β = 90
c = 254.546γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-HL080050
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117263-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence