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- EMDB-20374: CryoEM structure of zebra fish alpha-1 glycine receptor bound wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-20374
TitleCryoEM structure of zebra fish alpha-1 glycine receptor bound with taurine in nanodisc, desensitized state
Map datazebra fish alpha-1 glycine receptor bound with taurine in nanodisc, desensitized
Sample
  • Complex: glycine receptor in complex with taurine
    • Protein or peptide: Glycine receptor subunit alphaZ1
  • Ligand: 2-AMINOETHANESULFONIC ACID
  • Ligand: UNKNOWN LIGAND
Keywordsglycine receptor / nanodisc / CryoEM / MEMBRANE PROTEIN
Function / homology
Function and homology information


transmitter-gated monoatomic ion channel activity / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding / chloride channel complex ...transmitter-gated monoatomic ion channel activity / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding / chloride channel complex / ligand-gated monoatomic ion channel activity / transmembrane transporter complex / response to amino acid / monoatomic ion transport / chloride transmembrane transport / central nervous system development / cellular response to amino acid stimulus / transmembrane signaling receptor activity / perikaryon / postsynaptic membrane / neuron projection / dendrite / synapse / zinc ion binding / membrane / plasma membrane
Similarity search - Function
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 ...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 subunit alphaZ1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYu J / Zhu H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100400 United States
CitationJournal: Cell / Year: 2021
Title: Mechanism of gating and partial agonist action in the glycine receptor.
Authors: Jie Yu / Hongtao Zhu / Remigijus Lape / Timo Greiner / Juan Du / Wei Lü / Lucia Sivilotti / Eric Gouaux /
Abstract: Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters ...Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters that produce maximum open channel probabilities (Po) are full agonists, whereas those that yield lower than maximum Po are partial agonists. Cys-loop receptors are an important class of neurotransmitter receptors, yet a structure-based understanding of the mechanism of partial agonist action has proven elusive. Here, we study the glycine receptor with the full agonist glycine and the partial agonists taurine and γ-amino butyric acid (GABA). We use electrophysiology to show how partial agonists populate agonist-bound, closed channel states and cryo-EM reconstructions to illuminate the structures of intermediate, pre-open states, providing insights into previously unseen conformational states along the receptor reaction pathway. We further correlate agonist-induced conformational changes to Po across members of the receptor family, providing a hypothetical mechanism for partial and full agonist action at Cys-loop receptors.
History
DepositionJul 1, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseJan 6, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.37
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pls
  • Surface level: 5.37
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20374.png

Downloads & links

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Map

FileDownload / File: emd_20374.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationzebra fish alpha-1 glycine receptor bound with taurine in nanodisc, desensitized
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å		0.91 Å/pix.
x 360 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.37 / Movie #1: 5.37
Minimum - Maximum-22.039652 - 39.063209999999998
Average (Standard dev.)0.002781145 (±1.0561324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.910.910.91
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z327.600327.600327.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-22.04039.0630.003

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Supplemental data

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Sample components

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Entire : glycine receptor in complex with taurine

EntireName: glycine receptor in complex with taurine
Components
  • Complex: glycine receptor in complex with taurine
    • Protein or peptide: Glycine receptor subunit alphaZ1
  • Ligand: 2-AMINOETHANESULFONIC ACID
  • Ligand: UNKNOWN LIGAND

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Supramolecule #1: glycine receptor in complex with taurine

SupramoleculeName: glycine receptor in complex with taurine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Glycine receptor subunit alphaZ1

MacromoleculeName: Glycine receptor subunit alphaZ1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 52.537598 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 subunit alphaZ1

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Macromolecule #3: 2-AMINOETHANESULFONIC ACID

MacromoleculeName: 2-AMINOETHANESULFONIC ACID / type: ligand / ID: 3 / Number of copies: 5 / Formula: TAU
Molecular weightTheoretical: 125.147 Da
Chemical component information

ChemComp-TAU:
2-AMINOETHANESULFONIC ACID

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Macromolecule #4: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 4 / Number of copies: 60 / Formula: UNL
Molecular weightTheoretical: 184.361 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79709
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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