3SQ6

Crystal Structures of the Ligand Binding Domain of a Pentameric Alpha7 Nicotinic Receptor Chimera with its Agonist Epibatidine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

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Literature

Ligand-binding domain of an alpha 7-nicotinic receptor chimera and its complex with agonist.

Li, S.X., Huang, S., Bren, N., Noridomi, K., Dellisanti, C.D., Sine, S.M., Chen, L.

(2011) Nat Neurosci 14: 1253-1259

  • DOI: https://doi.org/10.1038/nn.2908
  • Primary Citation of Related Structures:  
    3SQ6, 3SQ9

  • PubMed Abstract: 

    The α(7) acetylcholine receptor (AChR) mediates pre- and postsynaptic neurotransmission in the central nervous system and is a potential therapeutic target in neurodegenerative, neuropsychiatric and inflammatory disorders. We determined the crystal structure of the extracellular domain of a receptor chimera constructed from the human α(7) AChR and Lymnaea stagnalis acetylcholine binding protein (AChBP), which shares 64% sequence identity and 71% similarity with native α(7). We also determined the structure with bound epibatidine, a potent AChR agonist. Comparison of the structures revealed molecular rearrangements and interactions that mediate agonist recognition and early steps in signal transduction in α(7) AChRs. The structures further revealed a ring of negative charge within the central vestibule, poised to contribute to cation selectivity. Structure-guided mutational studies disclosed distinctive contributions to agonist recognition and signal transduction in α(7) AChRs. The structures provide a realistic template for structure-aided drug design and for defining structure-function relationships of α(7) AChRs.

    • Organizational Affiliation: 

    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuronal acetylcholine receptor subunit alpha-7, Acetylcholine-binding protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
204Homo sapiens, Lymnaea stagnalis
This entity is chimeric		Mutation(s): 0 
Gene Names: CHRNA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
EA [auth H]
GA [auth I]
M [auth A]
BA [auth G],
DA [auth H],
EA [auth H],
GA [auth I],
M [auth A],
N [auth A],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
V [auth D],
X [auth E],
Z [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EPJ
Query on EPJ
Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
FA [auth I]
HA [auth J]
L [auth A]
AA [auth G],
CA [auth H],
FA [auth I],
HA [auth J],
L [auth A],
O [auth B],
R [auth C],
U [auth D],
W [auth E],
Y [auth F]
EPIBATIDINE
C11 H13 Cl N2
NLPRAJRHRHZCQQ-IVZWLZJFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.237α = 90
b = 141.069β = 99.65
c = 130.207γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary