5SXV | pdb_00005sxv

X-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion channel (ELIC) in a resting state

• PDB DOI: https://doi.org/10.2210/pdb5SXV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Dickeya chrysanthemi
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2016-08-10 Released: 2017-06-21 
• Deposition Author(s): Chen, Q., Kinde, M., Cohen, A., Xu, Y., Tang, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.259 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of Alcohol Inhibition of the Pentameric Ligand-Gated Ion Channel ELIC.

Chen, Q., Wells, M.M., Tillman, T.S., Kinde, M.N., Cohen, A., Xu, Y., Tang, P.

(2017) Structure 25: 180-187

• PubMed: 27916519 
• DOI: https://doi.org/10.1016/j.str.2016.11.007
• Primary Citation Related Structures: 
  5SXU, 5SXV


• PubMed Abstract: 
  

  The structural basis for alcohol modulation of neuronal pentameric ligand-gated ion channels (pLGICs) remains elusive. We determined an inhibitory mechanism of alcohol on the pLGIC Erwinia chrysanthemi (ELIC) through direct binding to the pore. X-ray structures of ELIC co-crystallized with 2-bromoethanol, in both the absence and presence of agonist, reveal 2-bromoethanol binding in the pore near T237(6') and the extracellular domain (ECD) of each subunit at three different locations. Binding to the ECD does not appear to contribute to the inhibitory action of 2-bromoethanol and ethanol as indicated by the same functional responses of wild-type ELIC and mutants. In contrast, the ELIC-α1β3GABA _A R chimera, replacing the ELIC transmembrane domain (TMD) with the TMD of α1β3GABA _A R, is potentiated by 2-bromoethanol and ethanol. The results suggest a dominant role of the TMD in modulating alcohol effects. The X-ray structures and functional measurements support a pore-blocking mechanism for inhibitory action of short-chain alcohols.

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Organizational Affiliation: 
• Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address: [e-mail].

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 374.74 kDa 
• Atom Count: 25,418 
• Modeled Residue Count: 3,080 
• Deposited Residue Count: 3,220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cys-loop ligand-gated ion channel	A, B, C, D, E, F, G, H, I, J	322	Dickeya chrysanthemi	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi) Explore P0C7B7  Go to UniProtKB:  P0C7B7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	EA [auth E], IA [auth F], NA [auth G], Q [auth B], R [auth B], RA [auth H], VA [auth I], Y [auth D], Z [auth D], ZA [auth J]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
BRJ	AA [auth E], BA [auth E], CA [auth E], DA [auth E], FA [auth F], GA [auth F], HA [auth F], JA [auth G], K [auth A], KA [auth G], L [auth A], LA [auth G], M [auth A], MA [auth G], N [auth B], O [auth B], OA [auth H], P [auth B], PA [auth H], QA [auth H], S [auth C], SA [auth I], T [auth C], TA [auth I], U [auth C], UA [auth I], V [auth D], W [auth D], WA [auth J], X [auth D], XA [auth J], YA [auth J]	2-BROMOETHANOL C2 H5 Br O LDLCZOVUSADOIV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.259 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.747	α = 90
b = 266.935	β = 107.04
c = 111.416	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Chen, Q., Kinde, M., Cohen, A., Xu, Y., Tang, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM066358
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM056257
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM075770
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R37GM049202

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description