2BYS

CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA IN complex with lobeline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structures of Aplysia Achbp Complexes with Nicotinic Agonists and Antagonists Reveal Distinctive Binding Interfaces and Conformations.

Hansen, S.B.Sulzenbacher, G.Huxford, T.Marchot, P.Taylor, P.Bourne, Y.

(2005) EMBO J 24: 3635

  • DOI: https://doi.org/10.1038/sj.emboj.7600828
  • Primary Citation of Related Structures:  
    2BYN, 2BYP, 2BYQ, 2BYR, 2BYS

  • PubMed Abstract: 

    Upon ligand binding at the subunit interfaces, the extracellular domain of the nicotinic acetylcholine receptor undergoes conformational changes, and agonist binding allosterically triggers opening of the ion channel. The soluble acetylcholine-binding protein (AChBP) from snail has been shown to be a structural and functional surrogate of the ligand-binding domain (LBD) of the receptor. Yet, individual AChBP species display disparate affinities for nicotinic ligands. The crystal structure of AChBP from Aplysia californica in the apo form reveals a more open loop C and distinctive positions for other surface loops, compared with previous structures. Analysis of Aplysia AChBP complexes with nicotinic ligands shows that loop C, which does not significantly change conformation upon binding of the antagonist, methyllycaconitine, further opens to accommodate the peptidic antagonist, alpha-conotoxin ImI, but wraps around the agonists lobeline and epibatidine. The structures also reveal extended and nonoverlapping interaction surfaces for the two antagonists, outside the binding loci for agonists. This comprehensive set of structures reflects a dynamic template for delineating further conformational changes of the LBD of the nicotinic receptor.


  • Organizational Affiliation

    Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0636, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACETYLCHOLINE-BINDING PROTEIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
227Aplysia 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LOB
Query on LOB

Download Ideal Coordinates CCD File 
K [auth A]
L [auth B]
M [auth C]
N [auth D]
O [auth E]
K [auth A],
L [auth B],
M [auth C],
N [auth D],
O [auth E],
P [auth F],
Q [auth G],
R [auth H],
S [auth I],
T [auth J]
LOBELINE
C22 H27 N O2
MXYUKLILVYORSK-QHAWAJNXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LOB PDBBind:  2BYS Kd: 0.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.764α = 89.95
b = 85.731β = 97.33
c = 117.318γ = 106.64
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary