6HJ3 | pdb_00006hj3

Xray structure of GLIC in complex with fumarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.216 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6HJ3

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel.

Fourati, Z.Sauguet, L.Delarue, M.

(2020) Acta Crystallogr D Struct Biol 76: 668-675

  • DOI: https://doi.org/10.1107/S205979832000772X
  • Primary Citation Related Structures: 
    6HJ3, 6HJA, 6HJB, 6HJI, 6HJZ, 6HPP

  • PubMed Abstract: 

    GLIC is a bacterial homologue of the pentameric ligand-gated ion channels (pLGICs) that mediate the fast chemical neurotransmission of nerve signalling in eukaryotes. Because the activation and allosteric modulation features are conserved among prokaryotic and eukaryotic pLGICs, GLIC is commonly used as a model to study the allosteric transition and structural pharmacology of pLGICs. It has previously been shown that GLIC is inhibited by some carboxylic acid derivatives. Here, experimental evidence for carboxylate binding to GLIC is provided by solving its X-ray structures with a series of monocarboxylate and dicarboxylate derivatives, and two carboxylate-binding sites are described: (i) the `intersubunit' site that partially overlaps the canonical pLGIC orthosteric site and (ii) the `intrasubunit' vestibular site, which is only occupied by a subset of the described derivatives. While the intersubunit site is widely conserved in all pLGICs, the intrasubunit site is only conserved in cationic eukaryotic pLGICs. This study sheds light on the importance of these two extracellular modulation sites as potential drug targets in pLGICs.


  • Organizational Affiliation
    • Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France.

Macromolecule Content 

  • Total Structure Weight: 194.94 kDa 
  • Atom Count: 13,140 
  • Modeled Residue Count: 1,555 
  • Deposited Residue Count: 1,585 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proton-gated ion channel
A, B, C, D, E
317Gloeobacter violaceusMutation(s): 0 
Gene Names: glvIglr4197
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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC

Query on PLC



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
F [auth A]
G [auth A]
H [auth A]
AA [auth C],
BA [auth C],
F [auth A],
G [auth A],
H [auth A],
IA [auth D],
JA [auth D],
N [auth A],
PA [auth E],
QA [auth E],
RA [auth E],
S [auth B],
T [auth B],
U [auth B],
Z [auth C]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
LMT

Query on LMT



Download:Ideal Coordinates CCD File
EA [auth C]
HA [auth D]
M [auth A]
MA [auth D]
UA [auth E]
EA [auth C],
HA [auth D],
M [auth A],
MA [auth D],
UA [auth E],
X [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FUM

Query on FUM



Download:Ideal Coordinates CCD File
FA [auth C],
NA [auth D],
P [auth A],
Q [auth A],
WA [auth E]
FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth C]
GA [auth C]
I [auth A]
J [auth A]
K [auth A]
CA [auth C],
GA [auth C],
I [auth A],
J [auth A],
K [auth A],
KA [auth D],
O [auth A],
OA [auth D],
SA [auth E],
V [auth B],
VA [auth E],
Y [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
DA [auth C]
L [auth A]
LA [auth D]
R [auth B]
TA [auth E]
DA [auth C],
L [auth A],
LA [auth D],
R [auth B],
TA [auth E],
W [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.216 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.51α = 90
b = 132.65β = 102.08
c = 159.86γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance13-BSV8-0020

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2020-07-15
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations