1UW6

X-ray structure of acetylcholine binding protein (AChBP) in complex with nicotine

• PDB DOI:  https://doi.org/10.2210/pdb1UW6/pdb

• Classification: GLYCOPROTEIN
• Organism(s): Lymnaea stagnalis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2004-01-30 Released: 2004-03-25 
• Deposition Author(s): Celie, P.H.N., Van Rossum-fikkert, S.E., Van Dijk, W.J., Brejc, K., Smit, A.B., Sixma, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Nicotine and Carbamylcholine Binding to Nicotinic Acetylcholine Receptors as Studied in Achbp Crystal Structures

Celie, P.H.N., Van Rossum-Fikkert, S.E., Van Dijk, W.J., Brejc, K., Smit, A.B., Sixma, T.K.

(2004) Neuron 41: 907

• PubMed: 15046723 
• DOI: https://doi.org/10.1016/s0896-6273(04)00115-1
• Primary Citation of Related Structures:  
  1UV6, 1UW6, 1UX2


• PubMed Abstract: 
  

Nicotinic acetylcholine receptors are prototypes for the pharmaceutically important family of pentameric ligand-gated ion channels. Here we present atomic resolution structures of nicotine and carbamylcholine binding to AChBP, a water-soluble homolog of the ligand binding domain of nicotinic receptors and their family members, GABAA, GABAC, 5HT3 serotonin, and glycine receptors. Ligand binding is driven by enthalpy and is accompanied by conformational changes in the ligand binding site. Residues in the binding site contract around the ligand, with the largest movement in the C loop. As expected, the binding is characterized by substantial aromatic and hydrophobic contributions, but additionally there are close contacts between protein oxygens and positively charged groups in the ligands. The higher affinity of nicotine is due to a main chain hydrogen bond with the B loop and a closer packing of the aromatic groups. These structures will be useful tools for the development of new drugs involving nicotinic acetylcholine receptor-associated diseases.

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Related Citations: 

• Crystal Structure of an Ach-Binding Protein Reveals the Ligand-Binding Domain of Nicotinic Receptors
  Brejc, K., Van Dijk, W.J., Klaassen, R., Schuurmans, M., Van Der Oost, J., Smit, A.B., Sixma, T.K.
  (2001) Nature 411: 269

• A Glia-Derived Acetylcholine-Binding Protein that Modulates Synaptic Transmission
  Smit, A.B., Syed, N.I., Schaap, D., Van Minnen, J., Klumperman, J., Kits, K.S., Lodder, H., Van Der Schors, R.C., Van Elk, R., Sorgedrager, B., Brejc, K., Sixma, T.K., Geraerts, W.P.M.
  (2001) Nature 411: 261

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Organizational Affiliation: 

Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 4 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 483.76 kDa 
• Atom Count: 34,788 
• Modelled Residue Count: 4,134 
• Deposited Residue Count: 4,220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINE-BINDING PROTEIN	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	211	Lymnaea stagnalis	Mutation(s): 0
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154  Go to UniProtKB:  P58154

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCT	AA [auth G], BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], KA [auth Q], LA [auth R], MA [auth S], NA [auth T], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE C10 H14 N2 SNICXCGAKADSCV-JTQLQIEISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NCT	BindingDB:  1UW6	Ki: min: 63.1, max: 496 (nM) from 6 assay(s)
		Kd: min: 40.7, max: 479 (nM) from 5 assay(s)
	PDBBind:  1UW6	Kd: 45.2 (nM) from 1 assay(s)
	Binding MOAD:  1UW6	Kd: 45.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 233	α = 90
b = 267.422	β = 90
c = 73.139	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-25 
Deposition Author(s): Celie, P.H.N., Van Rossum-fikkert, S.E., Van Dijk, W.J., Brejc, K., Smit, A.B., Sixma, T.K.

Revision History  

• Version 1.0: 2004-03-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance