4XHE | pdb_00004xhe

Crystal Structure of A-AChBP in complex with pinnatoxin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.216 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Marine Macrocyclic Imines, Pinnatoxins A and G: Structural Determinants and Functional Properties to Distinguish Neuronal alpha 7 from Muscle alpha 12 beta gamma delta nAChRs.

Bourne, Y.Sulzenbacher, G.Radic, Z.Araoz, R.Reynaud, M.Benoit, E.Zakarian, A.Servent, D.Molgo, J.Taylor, P.Marchot, P.

(2015) Structure 23: 1106-1115

  • DOI: https://doi.org/10.1016/j.str.2015.04.009
  • Primary Citation Related Structures: 
    4XHE, 4XK9

  • PubMed Abstract: 

    Pinnatoxins are macrocyclic imine phycotoxins associated with algal blooms and shellfish toxicity. Functional analysis of pinnatoxin A and pinnatoxin G by binding and voltage-clamp electrophysiology on membrane-embedded neuronal α7, α4β2, α3β2, and muscle-type α12βγδ nicotinic acetylcholine receptors (nAChRs) reveals high-affinity binding and potent antagonism for the α7 and α12βγδ subtypes. The toxins also bind to the nAChR surrogate, acetylcholine-binding protein (AChBP), with low Kd values reflecting slow dissociation. Crystal structures of pinnatoxin-AChBP complexes (1.9-2.2 Å resolution) show the multiple anchoring points of the hydrophobic portion, the cyclic imine, and the substituted bis-spiroketal and cyclohexene ring systems of the pinnatoxins that dictate tight binding between the opposing loops C and F at the receptor subunit interface, as observed for the 13-desmethyl-spirolide C and gymnodimine A congeners. Uniquely, however, the bulky bridged EF-ketal ring specific to the pinnatoxins extends radially from the interfacial-binding pocket to interact with the sequence-variable loop F and govern nAChR subtype selectivity and central neurotoxicity.


  • Organizational Affiliation
    • Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, Campus Luminy, 13288 Marseille cedex 9, France; Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, Campus Luminy, 13288 Marseille cedex 9, France. Electronic address: yves.bourne@afmb.univ-mrs.fr.

Macromolecule Content 

  • Total Structure Weight: 254.59 kDa 
  • Atom Count: 19,628 
  • Modeled Residue Count: 2,115 
  • Deposited Residue Count: 2,170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Soluble acetylcholine receptor
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
217Aplysia californicaMutation(s): 0 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
40P

Query on 40P



Download:Ideal Coordinates CCD File
K [auth A]
L [auth B]
N [auth C]
O [auth D]
Q [auth E]
K [auth A],
L [auth B],
N [auth C],
O [auth D],
Q [auth E],
S [auth F],
T [auth G],
U [auth H],
V [auth I],
X [auth J]
Pinnatoxin A
C41 H61 N O9
ZYFHPTPXLHNGQK-OICTYLSBSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
M [auth B],
P [auth D],
W [auth I]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
R [auth E],
Y [auth J]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.216 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.734α = 90
b = 144.231β = 90
c = 147.121γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary