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- EMDB-20518: CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-20518
TitleCryoEM structure of zebra fish alpha-1 glycine receptor, Apo state
Map dataAlpha-1 glycine receptor, Apo state
Sample
  • Complex: glycine receptor
    • Protein or peptide: Glycine receptor subunit alphaZ1
  • Ligand: CHLORIDE ION
  • Ligand: water
Keywordsglycine receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / transmitter-gated monoatomic ion channel activity / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex ...Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / transmitter-gated monoatomic ion channel activity / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / chloride channel complex / ligand-gated monoatomic ion channel activity / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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: 2.9 Å
AuthorsDu J / Lu W
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 25, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseFeb 10, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.447
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.447
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6pxd
  • Surface level: 0.447
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20518.png

Downloads & links

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Map

FileDownload / File: emd_20518.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAlpha-1 glycine receptor, Apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å		1.04 Å/pix.
x 280 pix.
= 291.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.447 / Movie #1: 0.447
Minimum - Maximum-1.0590147 - 2.0008383
Average (Standard dev.)0.0032976894 (±0.052130822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 291.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z291.200291.200291.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-1.0592.0010.003

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Supplemental data

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Sample components

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Entire : glycine receptor

EntireName: glycine receptor
Components
  • Complex: glycine receptor
    • Protein or peptide: Glycine receptor subunit alphaZ1
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: glycine receptor

SupramoleculeName: glycine receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 200 kDa/nm

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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: 43.973926 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 AVNFIARAGT KLFISRAKRI DTVSRVAFPL VFLIFNIFYW ITYKLVPRGS HHHHHHHH

UniProtKB: Glycine receptor subunit alphaZ1, Glycine receptor subunit alphaZ1

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / 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 state2D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 9.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115864
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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