6HPP | pdb_00006hpp

X-ray structure of GLIC in complex with propionate

PDB DOI: https://doi.org/10.2210/pdb6HPP/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Gloeobacter violaceus PCC 7421
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2018-09-21 Released: 2019-10-09
Deposition Author(s): Fourati, Z., Delarue, M.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.201 (Depositor), 0.239 (DCC)
R-Value Work:
0.194 (Depositor), 0.224 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 32627739 Search on PubMed Search on PubMed Central
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: 185.58 kDa
Atom Count: 12,782
Modeled Residue Count: 1,555
Deposited Residue Count: 1,585
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton-gated ion channel	A, B, C, D, E	317	Gloeobacter violaceus PCC 7421	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NDN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain GA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C]	AA [auth D] GA [auth E] K [auth A] L [auth A] R [auth B] AA [auth D], GA [auth E], K [auth A], L [auth A], R [auth B], W [auth C]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AA [auth D] Focus chain GA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain W [auth C]
PPI Query on PPI Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain X [auth C]	BA [auth D] CA [auth D] DA [auth D] HA [auth E] M [auth A] BA [auth D], CA [auth D], DA [auth D], HA [auth E], M [auth A], N [auth A], O [auth A], S [auth B], T [auth B], X [auth C]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	EA [auth E] F [auth A] G [auth A] H [auth A] P [auth B] EA [auth E], F [auth A], G [auth A], H [auth A], P [auth B], U [auth C], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	FA [auth E] I [auth A] J [auth A] Q [auth B] V [auth C] FA [auth E], I [auth A], J [auth A], Q [auth B], V [auth C], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Z [auth D]