2XQA | pdb_00002xqa

Pentameric ligand gated ion channel GLIC in complex with tetrabutylantimony (TBSb)

• PDB DOI: https://doi.org/10.2210/pdb2XQA/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Gloeobacter violaceus PCC 7421
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2010-09-01 Released: 2010-11-10 
• Deposition Author(s): Hilf, R.J.C., Bertozzi, C., Zimmermann, I., Reiter, A., Trauner, D., Dutzler, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Structural Basis of Open Channel Block in a Prokaryotic Pentameric Ligand-Gated Ion Channel

Hilf, R.J.C., Bertozzi, C., Zimmermann, I., Reiter, A., Trauner, D., Dutzler, R.

(2010) Nat Struct Mol Biol 17: 1330

• PubMed: 21037567 
• DOI: https://doi.org/10.1038/nsmb.1933
• Primary Citation Related Structures: 
  2XQ3, 2XQ4, 2XQ5, 2XQ6, 2XQ7, 2XQ8, 2XQ9, 2XQA


• PubMed Abstract: 
  

  The flow of ions through cation-selective members of the pentameric ligand-gated ion channel family is inhibited by a structurally diverse class of molecules that bind to the transmembrane pore in the open state of the protein. To obtain insight into the mechanism of channel block, we have investigated the binding of positively charged inhibitors to the open channel of the bacterial homolog GLIC by using X-ray crystallography and electrophysiology. Our studies reveal the location of two regions for interactions, with larger blockers binding in the center of the membrane and divalent transition metal ions binding to the narrow intracellular pore entry. The results provide a structural foundation for understanding the interactions of the channel with inhibitors that is relevant for the entire family.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zürich, Zürich, Switzerland.

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: 181.51 kDa 
• Atom Count: 12,606 
• Modeled Residue Count: 1,550 
• Deposited Residue Count: 1,585 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLR4197 PROTEIN	A, B, C, D, E	317	Gloeobacter violaceus PCC 7421	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NDN8  Go to UniProtKB:  Q7NDN8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SB	F [auth E]	ANTIMONY (III) ION Sb FAWGZAFXDJGWBB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.314	α = 90
b = 128.31	β = 104.04
c = 164.374	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Hilf, R.J.C., Bertozzi, C., Zimmermann, I., Reiter, A., Trauner, D., Dutzler, R.

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-05-19
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-05-08
  Changes: Data collection, Database references, Other