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- EMDB-20377: CryoEM structure of zebra fish alpha-1 glycine receptor bound wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-20377
TitleCryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA in nanodisc, closed state
Map datazebra fish alpha-1 glycine receptor bound with GABA in nanodisc, closed state
Sample
  • Complex: glycine receptor in complex with GABA
    • Protein or peptide: Glycine receptor subunit alphaZ1
  • Ligand: UNKNOWN LIGAND
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
Keywordsglycine receptor / nanodisc / CryoEM / 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 / transmitter-gated monoatomic ion channel activity / regulation of neuron differentiation / ligand-gated monoatomic ion channel activity / glycine binding / cellular response to zinc ion / cellular response to ethanol / response to amino acid ...Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / transmitter-gated monoatomic ion channel activity / regulation of neuron differentiation / ligand-gated monoatomic ion channel activity / glycine binding / cellular response to zinc ion / cellular response to ethanol / response to amino acid / chloride channel complex / monoatomic ion transport / chloride transmembrane transport / central nervous system development / cellular response to amino acid stimulus / transmembrane signaling receptor activity / perikaryon / postsynaptic membrane / dendrite / 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: 3.3 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: Yu J / Zhu H / Lape R / Greiner T / Du J / Lu W / Sivilotti L / Gouaux E
History
DepositionJul 1, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseJan 6, 2021-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.64
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.64
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6plv
  • Surface level: 5.64
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_20377.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationzebra fish alpha-1 glycine receptor bound with GABA in nanodisc, closed state
Voxel sizeX=Y=Z: 0.91 Å
Density
Contour LevelBy AUTHOR: 5.64 / Movie #1: 5.64
Minimum - Maximum-16.26803 - 32.729579999999999
Average (Standard dev.)-0.005753204 (±0.73860407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 364.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.910.910.91
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z364.000364.000364.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-16.26832.730-0.006

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Supplemental data

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Sample components

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Entire : glycine receptor in complex with GABA

EntireName: glycine receptor in complex with GABA
Components
  • Complex: glycine receptor in complex with GABA
    • Protein or peptide: Glycine receptor subunit alphaZ1
  • Ligand: UNKNOWN LIGAND
  • Ligand: GAMMA-AMINO-BUTANOIC ACID

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Supramolecule #1: glycine receptor in complex with GABA

SupramoleculeName: glycine receptor in complex with GABA / 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: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 3 / Number of copies: 60 / Formula: UNL
Molecular weightTheoretical: 142.282 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #4: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 4 / Number of copies: 5 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID

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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38383
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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