2XZ5 | pdb_00002xz5

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

• PDB DOI: https://doi.org/10.2210/pdb2XZ5/pdb

• Classification: RECEPTOR
• Organism(s): Aplysia californica
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-11-23 Released: 2010-12-08 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.219 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

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 Biological Chem 286: 4420

• PubMed: 21115477 
• DOI: https://doi.org/10.1074/jbc.M110.188730
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Structural Neurobiology, KULeuven, 3000 Leuven, Belgium.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 127.23 kDa 
• Atom Count: 8,725 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,085 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SOLUBLE ACETYLCHOLINE RECEPTOR	A, B, C, D, E	217	Aplysia californica	Mutation(s): 1
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8  Go to UniProtKB:  Q8WSF8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	EA [auth D], FA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACH	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	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	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	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
ID	Chains	Type	Formula	2D Diagram	Parent
SCH	A, B, C, D, E	L-PEPTIDE LINKING	C4 H9 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.219 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.123	α = 90
b = 119.405	β = 90
c = 267.744	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): 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.

Revision History  

• 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