9PKX | pdb_00009pkx

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 500 nM ivermectin

PDB DOI: https://doi.org/10.2210/pdb9PKX/pdb
EM Map EMD-71706: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Danio rerio
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): No

Deposited: 2025-07-14 Released: 2026-01-07
Deposition Author(s): Gibbs, E., Chakrapani, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for domain coupling in heteromeric glycine receptors revealed by an atypical allosteric agonist.

Gibbs, E., Feddersen, B., Kindig, K.J., Seiferth, D., Biggin, P.C., Chakrapani, S.

(2026) Sci Adv 12: eaeb2036-eaeb2036

PubMed: 41686897 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aeb2036
Primary Citation Related Structures:
9PKW, 9PKX, 9PKY, 9PKZ

PubMed Abstract:
Glycine receptors (GlyRs), pentameric ligand-gated ion channels (pLGICs), mediate sensory and motor functions. GlyR functional states are well characterized; however, structural details of transitions between states remain undefined. Here, we determined cryo-electron microscopy structures of GlyRα1β (with gephyrin E-domain) at varying concentrations of ivermectin, a transmembrane domain (TMD) allosteric agonist, and at saturating concentrations of strychnine, a competitive antagonist at the extracellular domain (ECD). Electrophysiology shows that ivermectin activates GlyR even with strychnine present. Structures with both ligands reveal intermediate states featuring a desensitized TMD and an ECD between closed and desensitized conformations, providing insights into domain cooperativity and ligand efficacy. Molecular dynamics simulations show how ivermectin affects strychnine dynamics. These data support a model where ivermectin activates GlyRs through a concerted and near-symmetric TMD mechanism, whereas allosteric ECD motions are graded and spatially heterogeneous. These findings reveal unanticipated features of GlyR gating and establish principles of allosteric modulation applicable to pLGICs.

Organizational Affiliation

Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106-4970, USA.

Macromolecule Content

Total Structure Weight: 278.75 kDa
Atom Count: 13,843
Modeled Residue Count: 1,683
Deposited Residue Count: 2,423
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor, alpha 1	A, B [auth D], C, D [auth B]	458	Danio rerio	Mutation(s): 0 Gene Names: glra1
UniProt
Find proteins for B3DHZ5 (Danio rerio) Explore B3DHZ5 Go to UniProtKB: B3DHZ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3DHZ5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B [auth D] Focus chain C Focus chain D [auth B]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor beta subunit 2	E	591	Danio rerio	Mutation(s): 0 Gene Names: glrbb, glrb2
UniProt
Find proteins for Q6DC22 (Danio rerio) Explore Q6DC22 Go to UniProtKB: Q6DC22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DC22
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SY9 (Subject of Investigation/LOI) Query on SY9 Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain K [auth B] SDF format, chain I [auth C] SDF format, chain F [auth A] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain K [auth B] MOL2 format, chain I [auth C] MOL2 format, chain F [auth A] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain K [auth B] mmCIF format, chain I [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth C], K [auth B], M [auth E], N [auth E]	STRYCHNINE C₂₁ H₂₂ N₂ O₂ QMGVPVSNSZLJIA-FVWCLLPLSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain K [auth B] Focus chain M [auth E] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain K [auth B] Focus chain M [auth E] Focus chain N [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain L [auth B] SDF format, chain J [auth C] SDF format, chain H [auth D] SDF format, chain G [auth A] MOL2 format, chain O [auth E] MOL2 format, chain L [auth B] MOL2 format, chain J [auth C] MOL2 format, chain H [auth D] MOL2 format, chain G [auth A] mmCIF format, chain O [auth E] mmCIF format, chain L [auth B] mmCIF format, chain J [auth C] mmCIF format, chain H [auth D] mmCIF format, chain G [auth A]	G [auth A], H [auth D], J [auth C], L [auth B], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth D] Focus chain J [auth C] Focus chain L [auth B] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth D] Focus chain J [auth C] Focus chain L [auth B] Focus chain O [auth E]