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- EMDB-72689: Homomeric Glycine Receptor alpha2 with PTX in an Apo State -

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Basic information

Entry
Database: EMDB / ID: EMD-72689
TitleHomomeric Glycine Receptor alpha2 with PTX in an Apo State
Map data
Sample
  • Complex: Homomeric Glycine Receptor alpha2 with PTX in an Apo State
    • Protein or peptide: Glycine receptor subunit alpha-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (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
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 / postsynaptic specialization membrane / glycine binding / cellular response to zinc ion / cellular response to ethanol / chloride channel complex / cell projection ...glycine-gated chloride ion channel activity / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycinergic synapse / postsynaptic specialization membrane / glycine binding / cellular response to zinc ion / cellular response to ethanol / chloride channel complex / cell projection / chloride transmembrane transport / neuropeptide signaling pathway / cellular response to amino acid stimulus / 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 / intracellular membrane-bounded organelle / 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, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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: 3.45 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)1F30HD114399-01 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 GlyRa2 Pore Dynamics in Gating and Inhibition
Authors: Klemm E / Gibbs E / Stauffer M / Mohapatra D / Meyer C / Chakrapani S
History
DepositionSep 13, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72689.png

Downloads & links

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Map

FileDownload / File: emd_72689.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.01309825 - 0.021316037
Average (Standard dev.)0.00002547551 (±0.00081849215)
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_72689_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72689_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72689_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homomeric Glycine Receptor alpha2 with PTX in an Apo State

EntireName: Homomeric Glycine Receptor alpha2 with PTX in an Apo State
Components
  • Complex: Homomeric Glycine Receptor alpha2 with PTX in an Apo State
    • Protein or peptide: Glycine receptor subunit alpha-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (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

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Supramolecule #1: Homomeric Glycine Receptor alpha2 with PTX in an Apo State

SupramoleculeName: Homomeric Glycine Receptor alpha2 with PTX in an Apo 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: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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 #3: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / 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 #4: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-...

MacromoleculeName: (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
type: ligand / ID: 4 / Number of copies: 1 / Formula: RI5
Molecular weightTheoretical: 292.284 Da

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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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.19.2_4158) / Number images used: 102851
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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