4UXU

Crystal Structure of the Extracellular Domain of the Human Alpha9 Nicotinic Acetylcholine Receptor In Complex with Methyllycaconitine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Crystal Structures of Free and Antagonist-Bound States of Human Alpha9 Nicotinic Receptor Extracellular Domain

Zouridakis, M.Giastas, P.Zarkadas, E.Chroni-Tzartou, D.Bregestovski, P.Tzartos, S.J.

(2014) Nat Struct Mol Biol 21: 976

  • DOI: https://doi.org/10.1038/nsmb.2900

  • PubMed Abstract: 

    We determined the X-ray crystal structures of the extracellular domain (ECD) of the monomeric state of human neuronal α9 nicotinic acetylcholine receptor (nAChR) and of its complexes with the antagonists methyllycaconitine and α-bungarotoxin at resolutions of 1.8 Å, 1.7 Å and 2.7 Å, respectively. The structure of the monomeric α9 ECD superimposed well with the structures of homologous proteins in pentameric assemblies, denoting native folding, despite the absence of a complementary subunit and transmembrane domain. The interaction motifs of both antagonists were similar to those in the complexes with homologous pentameric proteins, thus highlighting the major contribution of the principal side of α9 ECD to their binding. The structures revealed a functionally important β7-β10 strand interaction in α9-containing nAChRs, involving their unique Thr147, a hydration pocket similar to that of mouse α1 ECD and a membrane-facing network coordinated by the invariant Arg210.


  • Organizational Affiliation

    Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
A, B
218Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGM1 (Homo sapiens)
Explore Q9UGM1 
Go to UniProtKB:  Q9UGM1
PHAROS:  Q9UGM1
GTEx:  ENSG00000174343 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGM1
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9UGM1-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLK
Query on MLK

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
METHYLLYCACONITINE
C37 H50 N2 O10
XLTANAWLDBYGFU-VTLKBQQISA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
L [auth B],
N [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
P [auth B],
Q [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.434α = 90
b = 66.246β = 102.76
c = 75.191γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2014-10-15
    Changes: Database references
  • Version 1.3: 2014-11-19
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-11-06
    Changes: Structure summary