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- EMDB-44964: Homomeric alpha3 glycine receptor in the presence of 0.1 mM glyci... -

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Basic information

Entry
Database: EMDB / ID: EMD-44964
TitleHomomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in an apo state
Map data
Sample
  • Complex: Pentameric Assembly of Human Glycine Receptor Subtype Alpha3
    • Protein or peptide: Glycine receptor subunit alpha-3
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • 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: GLYCINE
  • 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 / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / 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 / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / chloride transmembrane transport / protein homooligomerization / transmembrane signaling receptor activity / perikaryon / postsynaptic membrane / neuron projection / intracellular membrane-bounded organelle / dendrite / synapse / 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: 2.19 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: To Be Published
Title: Physiological modulation of alpha3 glycine receptors
Authors: Kindig K / Gibbs E / Chakrapani S
History
DepositionMay 21, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44964.png

Downloads & links

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Map

FileDownload / File: emd_44964.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: 0.012
Minimum - Maximum-0.02422819 - 0.07543538
Average (Standard dev.)0.00005145908 (±0.0025782408)
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_44964_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44964_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 : 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: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • 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: GLYCINE
  • 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: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 25 / 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: [(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: 5 / 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: GLYCINE

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

ChemComp-GLY:
GLYCINE

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 35 / 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

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: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132119
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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