5OUG

Humanized alpha-AChBP (acetylcholine binding protein) in complex with lobeline and allosteric binder fragment 4.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

An allosteric binding site of the alpha 7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein.

Delbart, F.Brams, M.Gruss, F.Noppen, S.Peigneur, S.Boland, S.Chaltin, P.Brandao-Neto, J.von Delft, F.Touw, W.G.Joosten, R.P.Liekens, S.Tytgat, J.Ulens, C.

(2018) J Biol Chem 293: 2534-2545

  • DOI: https://doi.org/10.1074/jbc.M117.815316
  • Primary Citation of Related Structures:  
    5OUG, 5OUH, 5OUI

  • PubMed Abstract: 

    Nicotinic acetylcholine receptors (nAChRs) belong to the family of pentameric ligand-gated ion channels and mediate fast excitatory transmission in the central and peripheral nervous systems. Among the different existing receptor subtypes, the homomeric α7 nAChR has attracted considerable attention because of its possible implication in several neurological and psychiatric disorders, including cognitive decline associated with Alzheimer's disease or schizophrenia. Allosteric modulators of ligand-gated ion channels are of particular interest as therapeutic agents, as they modulate receptor activity without affecting normal fluctuations of synaptic neurotransmitter release. Here, we used X-ray crystallography and surface plasmon resonance spectroscopy of α7-acetylcholine-binding protein (AChBP), a humanized chimera of a snail AChBP, which has 71% sequence similarity with the extracellular ligand-binding domain of the human α7 nAChR, to investigate the structural determinants of allosteric modulation. We extended previous observations that an allosteric site located in the vestibule of the receptor offers an attractive target for receptor modulation. We introduced seven additional humanizing mutations in the vestibule-located binding site of AChBP to improve its suitability as a model for studying allosteric binding. Using a fragment-based screening approach, we uncovered an allosteric binding site located near the β8-β9 loop, which critically contributes to coupling ligand binding to channel opening in human α7 nAChR. This work expands our understanding of the topology of allosteric binding sites in AChBP and, by extrapolation, in the human α7 nAChR as determined by electrophysiology measurements. Our insights pave the way for drug design strategies targeting nAChRs involved in ion channel-mediated disorders.


  • Organizational Affiliation

    From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Humanized alpha-AChBP
A, B, C, D, E
205Homo sapiensMutation(s): 0 
Gene Names: CHRNA7NACHRA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L0B
Query on L0B

Download Ideal Coordinates CCD File 
K [auth A],
N [auth A],
Q [auth B],
T [auth C],
W [auth D]
Alpha-Lobeline
C22 H27 N O2
MXYUKLILVYORSK-HBMCJLEFSA-N
9Z0
Query on 9Z0

Download Ideal Coordinates CCD File 
L [auth A]
M [auth A]
O [auth B]
P [auth B]
R [auth C]
L [auth A],
M [auth A],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
X [auth E],
Y [auth E]
4,5-dibromo-N-(3-hydroxypropyl)-1H-pyrrole-2-carboxamide
C8 H10 Br2 N2 O2
UAVIBMSTKCBELE-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
Z [auth E]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.673α = 90
b = 119.806β = 107.29
c = 84.543γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KU LeuvenBelgiumC32/16/035

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary