6HYV

THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Y119A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel.

Hu, H., Ataka, K., Menny, A., Fourati, Z., Sauguet, L., Corringer, P.J., Koehl, P., Heberle, J., Delarue, M.

(2018) Proc Natl Acad Sci U S A 115: E12172-E12181

  • DOI: https://doi.org/10.1073/pnas.1813378116
  • Primary Citation of Related Structures:  
    6HY5, 6HY9, 6HYA, 6HYR, 6HYV, 6HYW, 6HYX, 6HYZ, 6HZ0, 6HZ1, 6HZ3, 6HZW, 6I08

  • PubMed Abstract: 

    • The pentameric ligand-gated ion channel (pLGIC) from Gloeobacter violaceus (GLIC) has provided insightful structure-function views on the permeation process and the allosteric regulation of the pLGICs family. However, GLIC is activated by pH instead of a neurotransmitter and a clear picture for the gating transition driven by protons is still lacking ...

    The pentameric ligand-gated ion channel (pLGIC) from Gloeobacter violaceus (GLIC) has provided insightful structure-function views on the permeation process and the allosteric regulation of the pLGICs family. However, GLIC is activated by pH instead of a neurotransmitter and a clear picture for the gating transition driven by protons is still lacking. We used an electrostatics-based (finite difference Poisson-Boltzmann/Debye-Hückel) method to predict the acidities of all aspartic and glutamic residues in GLIC, both in its active and closed-channel states. Those residues with a predicted pK a close to the experimental pH 50 were individually replaced by alanine and the resulting variant receptors were titrated by ATR/FTIR spectroscopy. E35, located in front of loop F far away from the orthosteric site, appears as the key proton sensor with a measured individual pK a at 5.8. In the GLIC open conformation, E35 is connected through a water-mediated hydrogen-bond network first to the highly conserved electrostatic triad R192-D122-D32 and then to Y197-Y119-K248, both located at the extracellular domain-transmembrane domain interface. The second triad controls a cluster of hydrophobic side chains from the M2-M3 loop that is remodeled during the gating transition. We solved 12 crystal structures of GLIC mutants, 6 of them being trapped in an agonist-bound but nonconductive conformation. Combined with previous data, this reveals two branches of a continuous network originating from E35 that reach, independently, the middle transmembrane region of two adjacent subunits. We conclude that GLIC's gating proceeds by making use of loop F, already known as an allosteric site in other pLGICs, instead of the classic orthosteric site.

    Organizational Affiliation: 

    Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France; marc.delarue@pasteur.fr.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proton-gated ion channel
A, B, C, D, E
317Gloeobacter violaceus PCC 7421Mutation(s): 1 
Gene Names: glvI, glr4197
Membrane Entity: Yes 
UniProt
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NDN8 
Go to UniProtKB:  Q7NDN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NDN8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC
Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
H [auth A]
I [auth A]
JA [auth D]
BA [auth C],
CA [auth C],
H [auth A],
I [auth A],
JA [auth D],
KA [auth D],
RA [auth E],
S [auth B],
SA [auth E],
T [auth B]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O		 Ligand Interaction
LMT
Query on LMT
Download Ideal Coordinates CCD File 
F [auth A]
GA [auth C]
HA [auth D]
OA [auth D]
P [auth A]
F [auth A],
GA [auth C],
HA [auth D],
OA [auth D],
P [auth A],
PA [auth E],
Q [auth B],
WA [auth E],
X [auth B],
Y [auth C],
Z [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
AA [auth C]
FA [auth C]
G [auth A]
IA [auth D]
NA [auth D]
AA [auth C],
FA [auth C],
G [auth A],
IA [auth D],
NA [auth D],
O [auth A],
QA [auth E],
R [auth B],
VA [auth E],
W [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
DA [auth C]
J [auth A]
K [auth A]
L [auth A]
LA [auth D]
DA [auth C],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
TA [auth E],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
EA [auth C]
M [auth A]
MA [auth D]
N [auth A]
UA [auth E]
EA [auth C],
M [auth A],
MA [auth D],
N [auth A],
UA [auth E],
V [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.81α = 90
b = 132.38β = 102.22
c = 159.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2019-01-09
    Changes: Data collection, Database references