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- PDB-9y80: Homomeric Glycine Receptor alpha2 with PTX in a Desensitized State -

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Basic information

Entry
Database: PDB / ID: 9y80
TitleHomomeric Glycine Receptor alpha2 with PTX in a Desensitized State
ComponentsGlycine receptor subunit alpha-2
KeywordsTRANSPORT PROTEIN / homopentamer / ion channel / ligand gated ion channel
Function / homology
Function and homology information


glycine-gated chloride ion channel activity / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycinergic synapse / excitatory extracellular ligand-gated monoatomic ion channel activity / postsynaptic specialization membrane / glycine binding / cellular response to zinc ion / cellular response to ethanol / chloride channel complex ...glycine-gated chloride ion channel activity / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycinergic synapse / excitatory extracellular ligand-gated monoatomic ion channel activity / postsynaptic specialization membrane / glycine binding / cellular response to zinc ion / cellular response to ethanol / chloride channel complex / cell projection / chloride transmembrane transport / cellular response to amino acid stimulus / neuropeptide signaling pathway / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / modulation of chemical synaptic transmission / GABA-ergic synapse / transmembrane signaling receptor activity / monoatomic ion transmembrane transport / metal ion binding / plasma membrane
Similarity search - Function
Glycine receptor alpha2 / Glycine receptor alpha / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel ...Glycine receptor alpha2 / Glycine receptor alpha / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
GLYCINE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-RI5 / Glycine receptor subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsKlemm, E. / Gibbs, E. / Chakrapani, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1F30 HD114399-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R35 GM134896-06 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152319 United States
CitationJournal: Structure / Year: 2026
Title: Human GlyRα2 pore dynamics in gating and inhibition.
Authors: Emily Klemm / Eric Gibbs / Madeleine Stauffer / Devesh Mohapatra / Chloe Meyer / Sudha Chakrapani /
Abstract: Glycine receptors (GlyRs) mediate inhibitory neurotransmission in the central nervous system. The GlyRα2 subtype contributes to critical neural circuitry in early neurodevelopment and is also found ...Glycine receptors (GlyRs) mediate inhibitory neurotransmission in the central nervous system. The GlyRα2 subtype contributes to critical neural circuitry in early neurodevelopment and is also found in adults. GlyRα2 dysfunctions are implicated in neurodevelopmental disorders, including autism, epilepsy, and cognitive delays. GlyRα2 functional properties and pharmacology are distinct from GlyRα1, but the structural basis for these differences remains poorly defined. Here, we report cryo-electron microscopy structures of full-length, human GlyRα2 reconstituted in peptidiscs captured in multiple conformational states. In addition to symmetric resting and desensitized states, we resolved an asymmetric open state, previously observed only in heteromeric GlyRs. This suggests that asymmetry is intrinsic to GlyRα2, independent of β-subunit incorporation. Furthermore, we identified distinct conformations of GlyRα2 with the pore-blocker picrotoxin, providing new insights into allosteric interactions. These findings uncover the structural basis of GlyRα2 function, providing a foundation for understanding its role in development and in GlyRα2-associated disorders.
History
DepositionSep 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine receptor subunit alpha-2
B: Glycine receptor subunit alpha-2
C: Glycine receptor subunit alpha-2
D: Glycine receptor subunit alpha-2
E: Glycine receptor subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,97836
Polymers268,9145
Non-polymers13,06431
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glycine receptor subunit alpha-2


Mass: 53782.840 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRA2
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P23416
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-RI5 / (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione / PICROTOXIN


Mass: 292.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#5: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homomeric Glycine Receptor alpha2 with PTX in a Desensitized State
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.19.2_4158model refinement
13PHENIX1.19.2_41583D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100331 / Symmetry type: POINT

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