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- EMDB-71708: Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200... -

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Basic information

Entry
Database: EMDB / ID: EMD-71708
TitleAlpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 0.02 mM ivermectin
Map data
Sample
  • Complex: Glycine receptor alpha1/beta
    • Protein or peptide: Glycine receptor, alpha 1
    • Protein or peptide: Glycine receptor beta subunit 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside
  • Ligand: STRYCHNINE
KeywordsIon Channel / Pentameric / Glycine / Receptor / TRANSPORT PROTEIN
Function / homology
Function and homology information


extracellularly glycine-gated chloride channel activity / transmitter-gated monoatomic ion channel activity / glycine binding / chloride channel complex / transmembrane signaling receptor activity / intracellular protein localization / perikaryon / postsynaptic membrane / dendrite / metal ion binding / cytoplasm
Similarity search - Function
Glycine receptor beta / : / Glycine receptor alpha1 / 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 ...Glycine receptor beta / : / Glycine receptor alpha1 / 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, alpha 1 / Glycine receptor subunit beta
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsGibbs E / Chakrapani S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 0.02 mM ivermectin
Authors: Gibbs E / Chakrapani S
History
DepositionJul 14, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71708.png

Downloads & links

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Map

FileDownload / File: emd_71708.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: 0.004
Minimum - Maximum-0.014755345 - 0.027561264
Average (Standard dev.)0.000045969322 (±0.001014702)
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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Mask #1

Fileemd_71708_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71708_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: #1

Fileemd_71708_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 : Glycine receptor alpha1/beta

EntireName: Glycine receptor alpha1/beta
Components
  • Complex: Glycine receptor alpha1/beta
    • Protein or peptide: Glycine receptor, alpha 1
    • Protein or peptide: Glycine receptor beta subunit 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside
  • Ligand: STRYCHNINE

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Supramolecule #1: Glycine receptor alpha1/beta

SupramoleculeName: Glycine receptor alpha1/beta / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Glycine receptor, alpha 1

MacromoleculeName: Glycine receptor, alpha 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 52.537598 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MFALGIYLWE TIVFFSLAAS QQAAARKAAS PMPPSEFLDK LMGKVSGYDA RIRPNFKGPP VNVTCNIFIN SFGSIAETTM DYRVNIFLR QQWNDPRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHEVTTDN KLLRISKNGN VLYSIRITLV L ACPMDLKN ...String:
MFALGIYLWE TIVFFSLAAS QQAAARKAAS PMPPSEFLDK LMGKVSGYDA RIRPNFKGPP VNVTCNIFIN SFGSIAETTM DYRVNIFLR QQWNDPRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHEVTTDN KLLRISKNGN VLYSIRITLV L ACPMDLKN FPMDVQTCIM QLESFGYTMN DLIFEWDEKG AVQVADGLTL PQFILKEEKD LRYCTKHYNT GKFTCIEARF HL ERQMGYY LIQMYIPSLL IVILSWVSFW INMDAAPARV GLGITTVLTM TTQSSGSRAS LPKVSYVKAI DIWMAVCLLF VFS ALLEYA AVNFIARQHK ELLRFQRRRR HLKEDEAGDG RFSFAAYGMG PACLQAKDGM AIKGNNNNAP TSTNPPEKTV EEMR KLFIS RAKRIDTVSR VAFPLVFLIF NIFYWITYKI IRSEDIHKQL VPRGSHHHHH HHH

UniProtKB: Glycine receptor, alpha 1

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Macromolecule #2: Glycine receptor beta subunit 2

MacromoleculeName: Glycine receptor beta subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 65.820281 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MKALKVIFML LIICLWMEGG FTKEKSAKKW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGS WSHPQFEKEN LYFQGEKSAK KGKKKGKQVY CPSQLSSEDL ARVPANSTSN ILNKLLITYD PRIRPNFKGI P VEDRVNIF ...String:
MKALKVIFML LIICLWMEGG FTKEKSAKKW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGS WSHPQFEKEN LYFQGEKSAK KGKKKGKQVY CPSQLSSEDL ARVPANSTSN ILNKLLITYD PRIRPNFKGI P VEDRVNIF INSFGSIQET TMDYRVNIFL RQRWNDPRLR LPQDFKSDSL TVDPKMFKCL WKPDLFFANE KSANFHDVTQ EN ILLFIFR NGDVLISMRL SVTLSCPLDL TLFPMDTQRC KMQLESFGYT TDDLQFMWQS GDPVQMDEIA LPQFDIKQED IEY GNCTKY YAGTGYYTCV EVIFTLRRQV GFYMMGVYAP TLLIVVLSWL SFWINPDASA ARVPLGILSV LSLSSECTSL ASEL PKVSY VKAIDIWLIA CLLFGFASLV EYAVVQVMLN SPKLLEAERA KIATKEKAEG KTPAKNTING MGSTPIHVST LQVTE TRCK KVCTSKSDLR TNDFSIVGSL PRDFELSNFD CYGKPIEVGS AFSKSQAKNN KKPPPPKPVI PSAAKRIDLY ARALFP FSF LFFNVIYWSV YLENLYFQGT ETSQVAPA

UniProtKB: Glycine receptor subunit beta

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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: 5 / 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: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)...

MacromoleculeName: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H- ...Name: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside
type: ligand / ID: 4 / Number of copies: 5 / Formula: IVM
Molecular weightTheoretical: 875.093 Da

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Macromolecule #5: STRYCHNINE

MacromoleculeName: STRYCHNINE / type: ligand / ID: 5 / Number of copies: 5 / Formula: SY9
Molecular weightTheoretical: 334.412 Da
Chemical component information

ChemComp-SY9:
STRYCHNINE

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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 / Details: CryoSparc ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 129399
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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