5AFK

alpha7-AChBP in complex with lobeline and fragment 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.381 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Molecular Blueprint of Allosteric Binding Sites in a Homologue of the Agonist-Binding Domain of the Alpha7 Nicotinic Acetylcholine Receptor.

Spurny, R.Debaveye, S.Farinha, A.Veys, K.Vos, A.M.Gossas, T.Atack, J.Bertrand, S.Bertrand, D.Danielson, U.H.Tresadern, G.Ulens, C.

(2015) Proc.Natl.Acad.Sci.USA 112: E2543

  • DOI: 10.1073/pnas.1418289112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The α7 nicotinic acetylcholine receptor (nAChR) belongs to the family of pentameric ligand-gated ion channels and is involved in fast synaptic signaling. In this study, we take advantage of a recently identified chimera of the extracellular domain of ...

    The α7 nicotinic acetylcholine receptor (nAChR) belongs to the family of pentameric ligand-gated ion channels and is involved in fast synaptic signaling. In this study, we take advantage of a recently identified chimera of the extracellular domain of the native α7 nicotinic acetylcholine receptor and acetylcholine binding protein, termed α7-AChBP. This chimeric receptor was used to conduct an innovative fragment-library screening in combination with X-ray crystallography to identify allosteric binding sites. One allosteric site is surface-exposed and is located near the N-terminal α-helix of the extracellular domain. Ligand binding at this site causes a conformational change of the α-helix as the fragment wedges between the α-helix and a loop homologous to the main immunogenic region of the muscle α1 subunit. A second site is located in the vestibule of the receptor, in a preexisting intrasubunit pocket opposite the agonist binding site and corresponds to a previously identified site involved in positive allosteric modulation of the bacterial homolog ELIC. A third site is located at a pocket right below the agonist binding site. Using electrophysiological recordings on the human α7 nAChR we demonstrate that the identified fragments, which bind at these sites, can modulate receptor activation. This work presents a structural framework for different allosteric binding sites in the α7 nAChR and paves the way for future development of novel allosteric modulators with therapeutic potential.


    Organizational Affiliation

    Laboratory of Structural Neurobiology, Katholieke Universiteit Leuven, Leuven B-3000, Belgium;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7
A, B, C, D, E
205Homo sapiensLymnaea stagnalis
This entity is chimeric
Mutation(s): 0 
Gene Names: CHRNA7 (NACHRA7),
Find proteins for P36544 (Homo sapiens)
Go to Gene View: CHRNA7
Go to UniProtKB:  P36544
Find proteins for P58154 (Lymnaea stagnalis)
Go to UniProtKB:  P58154
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L0B
Query on L0B

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Download CCD File 
A, B, C, D, E
Alpha-Lobeline
C22 H27 N O2
MXYUKLILVYORSK-HBMCJLEFSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
5VU
Query on 5VU

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Download CCD File 
A, B, C, D, E
N-(2,4-difluorophenyl)pyrrolidine-1-carboxamide
C11 H12 F2 N2 O
CPBDOIXLUULXND-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.381 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.695α = 90.00
b = 112.293β = 90.00
c = 144.305γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references
  • Version 1.2: 2015-06-03
    Type: Database references
  • Version 1.3: 2017-03-15
    Type: Source and taxonomy
  • Version 1.4: 2017-03-22
    Type: Source and taxonomy