6F13

GLIC mutant E75A

PDB DOI: https://doi.org/10.2210/pdb6F13/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Gloeobacter violaceus PCC 7421
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2017-11-21 Released: 2018-01-10
Deposition Author(s): Hu, H.D., Delarue, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 ?
R-Value Free: 0.223
R-Value Work: 0.203
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel.

Nemecz, A., Hu, H., Fourati, Z., Van Renterghem, C., Delarue, M., Corringer, P.J.

(2017) PLoS Biol 15: e2004470-e2004470

PubMed: 29281623 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pbio.2004470
Primary Citation of Related Structures:
6F0I, 6F0J, 6F0M, 6F0N, 6F0R, 6F0U, 6F0V, 6F0Z, 6F10, 6F11, 6F12, 6F13, 6F15, 6F16

PubMed Abstract:
The Gloeobacter violaceus ligand-gated ion channel (GLIC) has been extensively studied by X-ray crystallography and other biophysical techniques. This provided key insights into the general gating mechanism of pentameric ligand-gated ion channel (pLGIC) signal transduction. However, the GLIC is activated by lowering the pH and the location of its putative proton activation site(s) still remain(s) unknown. To this end, every Asp, Glu, and His residue was mutated individually or in combination and investigated by electrophysiology. In addition to the mutational analysis, key mutations were structurally resolved to address whether particular residues contribute to proton sensing, or alternatively to GLIC-gating, independently of the side chain protonation. The data show that multiple residues located below the orthosteric site, notably E26, D32, E35, and D122 in the lower part of the extracellular domain (ECD), along with E222, H235, E243, and H277 in the transmembrane domain (TMD), alter GLIC activation. D122 and H235 were found to also alter GLIC expression. E35 is identified as a key proton-sensing residue, whereby neutralization of its side chain carboxylate stabilizes the active state. Thus, proton activation occurs allosterically to the orthosteric site, at the level of multiple loci with a key contribution of the coupling interface between the ECD and TMD.

Organizational Affiliation

Unité Récepteurs-Canaux, Unité Mixte de Recherche 3571 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France.

Macromolecule Content

Total Structure Weight: 193.86 kDa
Atom Count: 13,461
Modelled Residue Count: 1,555
Deposited Residue Count: 1,585
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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): 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NDN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLC Query on PLC Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain IA [auth D] SDF format, chain KA [auth D] SDF format, chain U [auth B] SDF format, chain BA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth D] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	AA [auth C] BA [auth C] CA [auth C] G [auth A] H [auth A] AA [auth C], BA [auth C], CA [auth C], G [auth A], H [auth A], I [auth A], IA [auth D], JA [auth D], KA [auth D], QA [auth E], RA [auth E], S [auth B], T [auth B], U [auth B]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain OA [auth D] SDF format, chain Q [auth B] SDF format, chain VA [auth E] SDF format, chain P [auth A] SDF format, chain Y [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain Y [auth B]	GA [auth C] OA [auth D] P [auth A] Q [auth B] VA [auth E] GA [auth C], OA [auth D], P [auth A], Q [auth B], VA [auth E], Y [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain GA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [auth B] Focus chain VA [auth E] Focus chain Y [auth B] Interactions & Density Focus chain GA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [auth B] Focus chain VA [auth E] Focus chain Y [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain Z [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain HA [auth D] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain PA [auth E] SDF format, chain R [auth B] SDF format, chain UA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain UA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain UA [auth E]	F [auth A] FA [auth C] HA [auth D] NA [auth D] O [auth A] F [auth A], FA [auth C], HA [auth D], NA [auth D], O [auth A], PA [auth E], R [auth B], UA [auth E], X [auth B], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain FA [auth C] Focus chain HA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain PA [auth E] Focus chain R [auth B] Focus chain UA [auth E] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain F [auth A] Focus chain FA [auth C] Focus chain HA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain PA [auth E] Focus chain R [auth B] Focus chain UA [auth E] Focus chain X [auth B] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain DA [auth C] SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain SA [auth E] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain V [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain SA [auth E] mmCIF format, chain V [auth B]	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], SA [auth E], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain SA [auth E] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain SA [auth E] Focus chain V [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain M [auth A] SDF format, chain TA [auth E] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain W [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain TA [auth E] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B]	EA [auth C] M [auth A] MA [auth D] N [auth A] TA [auth E] EA [auth C], M [auth A], MA [auth D], N [auth A], TA [auth E], W [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain TA [auth E] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain TA [auth E] Focus chain W [auth B]