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- EMDB-44963: Homomeric alpha3 glycine receptor in the presence of 0.1 mM glyci... -

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Basic information

Entry
Database: EMDB / ID: EMD-44963
TitleHomomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in a desensitized state
Map data
Sample
  • Complex: Pentameric Assembly of Human Glycine Receptor Subtype Alpha3
    • Protein or peptide: Glycine receptor subunit alpha-3
  • Ligand: GLYCINE
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
KeywordsGlycine / Ion Channel / Ligand-Gated / Pentameric / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycinergic synapse / glycine binding / presynaptic modulation of chemical synaptic transmission / chloride transmembrane transport / protein homooligomerization / transmembrane signaling receptor activity ...glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycinergic synapse / glycine binding / presynaptic modulation of chemical synaptic transmission / chloride transmembrane transport / protein homooligomerization / transmembrane signaling receptor activity / presynaptic membrane / perikaryon / postsynaptic membrane / intracellular membrane-bounded organelle / dendrite / metal ion binding / plasma membrane
Similarity search - Function
Glycine receptor alpha3 / 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 alpha3 / 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-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsKindig K / Gibbs E / Chakrapani S
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM131216 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM108921-03S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108921-5S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM131216-1S1 United States
National Institutes of Health/Office of the Director1S10OD032437 United States
CitationJournal: Sci Adv / Year: 2024
Title: Mechanisms underlying modulation of human GlyRα3 by Zn and pH.
Authors: Kayla Kindig / Eric Gibbs / David Seiferth / Philip C Biggin / Sudha Chakrapani /
Abstract: Glycine receptors (GlyRs) regulate motor control and pain processing in the central nervous system through inhibitory synaptic signaling. The subtype GlyRα3 expressed in nociceptive sensory neurons ...Glycine receptors (GlyRs) regulate motor control and pain processing in the central nervous system through inhibitory synaptic signaling. The subtype GlyRα3 expressed in nociceptive sensory neurons of the spinal dorsal horn is a key regulator of physiological pain perception. Disruption of spinal glycinergic inhibition is associated with chronic inflammatory pain states, making GlyRα3 an attractive target for pain treatment. GlyRα3 activity is modulated by numerous endogenous and exogenous ligands that consequently affect pain sensitization. To understand the mechanism of two such endogenous modulators, Zn and protons, we have used cryo-electron microscopy to determine structures of full-length human GlyRα3 in various functional states. Whereas acidic pH reduces peak glycine response, Zn displays biphasic modulation in a concentration-dependent manner. Our findings reveal the effector sites and also capture intermediate conformations in the gating cycle. Combined with molecular dynamics simulations and electrophysiology, this work provides important insights into GlyRα3 activation and regulation.
History
DepositionMay 21, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44963.png

Downloads & links

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Map

FileDownload / File: emd_44963.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. 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: 0.011
Minimum - Maximum-0.023899209 - 0.07748673
Average (Standard dev.)0.000055834138 (±0.0025655616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44963_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44963_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Pentameric Assembly of Human Glycine Receptor Subtype Alpha3

EntireName: Pentameric Assembly of Human Glycine Receptor Subtype Alpha3
Components
  • Complex: Pentameric Assembly of Human Glycine Receptor Subtype Alpha3
    • Protein or peptide: Glycine receptor subunit alpha-3
  • Ligand: GLYCINE
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: Pentameric Assembly of Human Glycine Receptor Subtype Alpha3

SupramoleculeName: Pentameric Assembly of Human Glycine Receptor Subtype Alpha3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Glycine receptor subunit alpha-3

MacromoleculeName: Glycine receptor subunit alpha-3 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.581066 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MAHVRHFRTL VSGFYFWEAA LLLSLVATKE TDSARSRSAP MSPSDFLDKL MGRTSGYDAR IRPNFKGPPV NVTCNIFINS FGSIAETTM DYRVNIFLRQ KWNDPRLAYS EYPDDSLDLD PSMLDSIWKP DLFFANEKGA NFHEVTTDNK LLRIFKNGNV L YSIRLTLT ...String:
MAHVRHFRTL VSGFYFWEAA LLLSLVATKE TDSARSRSAP MSPSDFLDKL MGRTSGYDAR IRPNFKGPPV NVTCNIFINS FGSIAETTM DYRVNIFLRQ KWNDPRLAYS EYPDDSLDLD PSMLDSIWKP DLFFANEKGA NFHEVTTDNK LLRIFKNGNV L YSIRLTLT LSCPMDLKNF PMDVQTCIMQ LESFGYTMND LIFEWQDEAP VQVAEGLTLP QFLLKEEKDL RYCTKHYNTG KF TCIEVRF HLERQMGYYL IQMYIPSLLI VILSWVSFWI NMDAAPARVA LGITTVLTMT TQSSGSRASL PKVSYVKAID IWM AVCLLF VFSALLEYAA VNFVSRQHKE LLRFRRKRKN KTEAFALEKF YRFSDMDDEV RESRFSFTAY GMGPCLQAKD GMTP KGPNH PVQVMPKSPD EMRKVFIDRA KKIDTISRAC FPLAFLIFNI FYWVIYKILR HEDIHQQQDL VPRGSHHHHH HHH

UniProtKB: Glycine receptor subunit alpha-3

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Macromolecule #3: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 3 / Number of copies: 5 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #4: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 4 / Number of copies: 25 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Macromolecule #5: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / 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 #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 40 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 6.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.0 µm / Nominal defocus min: 0.75 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: PDB ENTRY
PDB model - PDB ID:

5tio

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165143
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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