2XZ5

MMTS-modified Y53C mutant of Aplysia AChBP in complex with acetylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of a Cysteine-Modified Mutant in Loop D of Acetylcholine Binding Protein

Brams, M.Gay, E.A.Colon Saez, J.Guskov, A.Van Elk, R.Van Der Schors, R.C.Peigneur, S.Tytgat, J.Strelkov, S.V.Smit, A.B.Yakel, J.L.Ulens, C.

(2011) J Biol Chem 286: 4420

  • DOI: https://doi.org/10.1074/jbc.M110.188730
  • Primary Citation of Related Structures:  
    2XZ5, 2XZ6

  • PubMed Abstract: 

    Covalent modification of α7 W55C nicotinic acetylcholine receptors (nAChR) with the cysteine-modifying reagent [2-(trimethylammonium)ethyl] methanethiosulfonate (MTSET(+)) produces receptors that are unresponsive to acetylcholine, whereas methyl methanethiolsulfonate (MMTS) produces enhanced acetylcholine-gated currents. Here, we investigate structural changes that underlie the opposite effects of MTSET(+) and MMTS using acetylcholine-binding protein (AChBP), a homolog of the extracellular domain of the nAChR. Crystal structures of Y53C AChBP show that MTSET(+)-modification stabilizes loop C in an extended conformation that resembles the antagonist-bound state, which parallels our observation that MTSET(+) produces unresponsive W55C nAChRs. The MMTS-modified mutant in complex with acetylcholine is characterized by a contracted C-loop, similar to other agonist-bound complexes. Surprisingly, we find two acetylcholine molecules bound in the ligand-binding site, which might explain the potentiating effect of MMTS modification in W55C nAChRs. Unexpectedly, we observed in the MMTS-Y53C structure that ten phosphate ions arranged in two rings at adjacent sites are bound in the vestibule of AChBP. We mutated homologous residues in the vestibule of α1 GlyR and observed a reduction in the single channel conductance, suggesting a role of this site in ion permeation. Taken together, our results demonstrate that targeted modification of a conserved aromatic residue in loop D is sufficient for a conformational switch of AChBP and that a defined region in the vestibule of the extracellular domain contributes to ion conduction in anion-selective Cys-loop receptors.


  • Organizational Affiliation

    Laboratory of Structural Neurobiology, KULeuven, 3000 Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E
217Aplysia californicaMutation(s): 1 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth D],
FA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACH
Query on ACH

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
HA [auth E]
IA [auth E]
L [auth B]
F [auth A],
G [auth A],
HA [auth E],
IA [auth E],
L [auth B],
M [auth B],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
ACETYLCHOLINE
C7 H16 N O2
OIPILFWXSMYKGL-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
K [auth A]
MA [auth E]
Q [auth B]
CA [auth D],
DA [auth D],
K [auth A],
MA [auth E],
Q [auth B],
R [auth B],
W [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
I [auth A]
J [auth A]
KA [auth E]
AA [auth D],
BA [auth D],
I [auth A],
J [auth A],
KA [auth E],
LA [auth E],
O [auth B],
P [auth B],
U [auth C],
V [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth D],
H [auth A],
JA [auth E],
N [auth B],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SCH
Query on SCH
A, B, C, D, E
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Binding Affinity Annotations 
IDSourceBinding Affinity
ACH PDBBind:  2XZ5 Ki: 9.83e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.123α = 90
b = 119.405β = 90
c = 267.744γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Atomic model, Other, Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary