Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Hetero 10-mer - A5B5 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A5B1C1D1E1F1 

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

Macromolecule Content

• Total Structure Weight: 128.61 kDa 
• Atom Count: 10229 
• Modelled Residue Count: 1113 
• Deposited Residue Count: 1130 
• Unique protein chains: 2

2BYP

Crystal structure of Aplysia californica AChBP in complex with alpha- conotoxin ImI

• DOI: 10.2210/pdb2BYP/pdb

• Classification: RECEPTOR
• Organism(s): Aplysia californica, Conus imperialis
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2005-08-03 Released: 2005-10-05 
• Deposition Author(s): Hansen, S.B., Sulzenbacher, G., Huxford, T., Marchot, P., Taylor, P., Bourne, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.214 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

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

• PubMed: 16193063 
• DOI: 10.1038/sj.emboj.7600828
• Primary Citation of Related Structures:  
  2BYP, 2BYN, 2BYS, 2BYR, 2BYQ


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SOLUBLE ACETYLCHOLINE RECEPTOR	A, B, C, D, E	214	Aplysia californica	Mutation(s): 0
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8  Go to UniProtKB:  Q8WSF8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-CONOTOXIN IMI	F, G, H, I, J	12	Conus imperialis	Mutation(s): 0
UniProt
Find proteins for P50983 (Conus imperialis) Explore P50983  Go to UniProtKB:  P50983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CY3	F, G, H, I, J	L-PEPTIDE LINKING	C3 H8 N2 O S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.214 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.284	α = 90
b = 140.036	β = 90
c = 153.386	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2005-08-03 
• Released Date: 2005-10-05 
Deposition Author(s): Hansen, S.B., Sulzenbacher, G., Huxford, T., Marchot, P., Taylor, P., Bourne, Y.

Revision History  

• Version 1.0: 2005-10-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Version format compliance
• Version 1.2: 2019-04-03
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary