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- EMDB-72675: Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desens... -

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Basic information

Entry
Database: EMDB / ID: EMD-72675
TitleHomomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desensitized State
Map data
Sample
  • Complex: Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desensitized State
    • Protein or peptide: Glycine receptor subunit alpha-2
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE
Keywordshomopentamer / ion channel / ligand gated ion channel / TRANSPORT PROTEIN
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 receptor subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsKlemm E / Gibbs E / Chakrapani S
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72675.png

Downloads & links

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Map

FileDownload / File: emd_72675.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 304 pix.
= 255.36 Å		0.84 Å/pix.
x 304 pix.
= 255.36 Å		0.84 Å/pix.
x 304 pix.
= 255.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045
Minimum - Maximum-0.010597782 - 0.026358213
Average (Standard dev.)0.000022593338 (±0.00092443853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 255.35999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72675_msk_1.map
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Half map: #2

Fileemd_72675_half_map_1.map
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Half map: #1

Fileemd_72675_half_map_2.map
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Sample components

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Entire : Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desens...

EntireName: Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desensitized State
Components
  • Complex: Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desensitized State
    • Protein or peptide: Glycine receptor subunit alpha-2
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE

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Supramolecule #1: Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desens...

SupramoleculeName: Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desensitized State
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glycine receptor subunit alpha-2

MacromoleculeName: Glycine receptor subunit alpha-2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.78284 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MNRQLVNILT ALFAFFLETN HFRTAFCKDH DSRSGKQPSQ TLSPSDFLDK LMGRTSGYDA RIRPNFKGPP VNVTCNIFIN SFGSVTETT MDYRVNIFLR QQWNDSRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHDVTTDN KLLRISKNGK V LYSIRLTL ...String:
MNRQLVNILT ALFAFFLETN HFRTAFCKDH DSRSGKQPSQ TLSPSDFLDK LMGRTSGYDA RIRPNFKGPP VNVTCNIFIN SFGSVTETT MDYRVNIFLR QQWNDSRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHDVTTDN KLLRISKNGK V LYSIRLTL TLSCPMDLKN FPMDVQTCTM QLESFGYTMN DLIFEWLSDG PVQVAEGLTL PQFILKEEKE LGYCTKHYNT GK FTCIEVK FHLERQMGYY LIQMYIPSLL IVILSWVSFW INMDAAPARV ALGITTVLTM TTQSSGSRAS LPKVSYVKAI DIW MAVCLL FVFAALLEYA AVNFVSRQHK EFLRLRRRQK RQNKEEDVTR ESRFNFSGYG MGHCLQVKDG TAVKATPANP LPQP PKDGD AIKKKFVDRA KRIDTISRAA FPLAFLIFNI FYWITYKIIR HEDVHKKLVP RGSHHHHHHH H

UniProtKB: Glycine receptor subunit alpha-2

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Macromolecule #2: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 20 / Formula: PX4
Molecular weightTheoretical: 678.94 Da
Chemical component information

ChemComp-PX4:
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DMPC, phospholipid*YM

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.19.2_4158) / Number images used: 28087
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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