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- EMDB-23911: Cryo-EM reveals partially and fully assembled native glycine rece... -

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Basic information

Entry
Database: EMDB / ID: EMD-23911
TitleCryo-EM reveals partially and fully assembled native glycine receptors,homomeric tetramer
Map data
Sample
  • Complex: Native homomeric glycine receptor tetramer bound with 3D1 fab
    • Complex: Native homomeric glycine receptor tetramer
      • Protein or peptide: Glycine receptor alpha 1
    • Complex: 3D1 fab
      • Protein or peptide: 3D1 Fab Light Chain
      • Protein or peptide: 3D1 Fab Heavy Chain
  • Ligand: alpha-D-mannopyranose
  • Ligand: beta-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsglycine receptor / ion channel / homomeric tetramer / MEMBRANE PROTEIN / SIGNALING PROTEIN
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / taurine binding / negative regulation of transmission of nerve impulse / acrosome reaction / positive regulation of acrosome reaction / synaptic transmission, glycinergic / neuromuscular process controlling posture / inhibitory synapse / regulation of respiratory gaseous exchange by nervous system process / righting reflex ...Neurotransmitter receptors and postsynaptic signal transmission / taurine binding / negative regulation of transmission of nerve impulse / acrosome reaction / positive regulation of acrosome reaction / synaptic transmission, glycinergic / neuromuscular process controlling posture / inhibitory synapse / regulation of respiratory gaseous exchange by nervous system process / righting reflex / extracellularly glycine-gated chloride channel activity / glycinergic synapse / inhibitory postsynaptic potential / cellular response to ethanol / adult walking behavior / cellular response to zinc ion / glycine binding / startle response / chloride channel complex / neuronal action potential / neuropeptide signaling pathway / muscle contraction / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / visual perception / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / transmembrane signaling receptor activity / perikaryon / postsynaptic membrane / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / zinc ion binding
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 alpha 1
Similarity search - Component
Biological speciesSus scrofa (pig) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZhu H / Gouaux E
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: Nature / Year: 2021
Title: Architecture and assembly mechanism of native glycine receptors.
Authors: Hongtao Zhu / Eric Gouaux /
Abstract: Glycine receptors (GlyRs) are pentameric, 'Cys-loop' receptors that form chloride-permeable channels and mediate fast inhibitory signalling throughout the central nervous system. In the spinal cord ...Glycine receptors (GlyRs) are pentameric, 'Cys-loop' receptors that form chloride-permeable channels and mediate fast inhibitory signalling throughout the central nervous system. In the spinal cord and brainstem, GlyRs regulate locomotion and cause movement disorders when mutated. However, the stoichiometry of native GlyRs and the mechanism by which they are assembled remain unclear, despite extensive investigation. Here we report cryo-electron microscopy structures of native GlyRs from pig spinal cord and brainstem, revealing structural insights into heteromeric receptors and their predominant subunit stoichiometry of 4α:1β. Within the heteromeric pentamer, the β(+)-α(-) interface adopts a structure that is distinct from the α(+)-α(-) and α(+)-β(-) interfaces. Furthermore, the β-subunit contains a unique phenylalanine residue that resides within the pore and disrupts the canonical picrotoxin site. These results explain why inclusion of the β-subunit breaks receptor symmetry and alters ion channel pharmacology. We also find incomplete receptor complexes and, by elucidating their structures, reveal the architectures of partially assembled α-trimers and α-tetramers.
History
DepositionApr 29, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 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: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mlv
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7mlv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23911.png

Downloads & links

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Map

FileDownload / File: emd_23911.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330.4 Å		0.83 Å/pix.
x 400 pix.
= 330.4 Å		0.83 Å/pix.
x 400 pix.
= 330.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.129 / Movie #1: 0.14
Minimum - Maximum-0.1722732 - 0.49961278
Average (Standard dev.)0.0027288124 (±0.022132903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8260.8260.826
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z330.400330.400330.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1720.5000.003

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Supplemental data

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Sample components

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Entire : Native homomeric glycine receptor tetramer bound with 3D1 fab

EntireName: Native homomeric glycine receptor tetramer bound with 3D1 fab
Components
  • Complex: Native homomeric glycine receptor tetramer bound with 3D1 fab
    • Complex: Native homomeric glycine receptor tetramer
      • Protein or peptide: Glycine receptor alpha 1
    • Complex: 3D1 fab
      • Protein or peptide: 3D1 Fab Light Chain
      • Protein or peptide: 3D1 Fab Heavy Chain
  • Ligand: alpha-D-mannopyranose
  • Ligand: beta-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Native homomeric glycine receptor tetramer bound with 3D1 fab

SupramoleculeName: Native homomeric glycine receptor tetramer bound with 3D1 fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 400 KDa

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Supramolecule #2: Native homomeric glycine receptor tetramer

SupramoleculeName: Native homomeric glycine receptor tetramer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: 3D1 fab

SupramoleculeName: 3D1 fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: 3D1 Fab Light Chain

MacromoleculeName: 3D1 Fab Light Chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 11.743124 KDa
Recombinant expressionOrganism: Rattus norvegicus (Norway rat)
SequenceString:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVS TAVAWYQQKP GQSPKLLIYW ASTRHTGVPG RFTGSGSGTD YTLTISSVQA EDLSLYYCQ QHYSTPRTFG GGTKLEIK

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Macromolecule #2: 3D1 Fab Heavy Chain

MacromoleculeName: 3D1 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 12.983512 KDa
Recombinant expressionOrganism: Rattus norvegicus (Norway rat)
SequenceString:
QVQLQQSGAE LMKPGAAVKI SCKATGHTIS RYWIDWLKQR PGHGLEWIGE ILPGSGSTNY NEKFKGKATF TAEKSSNTAY MQLSSLTSE DSAVYYCAMG VRGNYFDYWG QGTTLTVSS

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Macromolecule #3: Glycine receptor alpha 1

MacromoleculeName: Glycine receptor alpha 1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 52.64475 KDa
SequenceString: MYRFNTLRLY LWETIVFFSL AASKEAEAAR SASKPMSPSD FLDKLMGRTS GYDARIRPNF KGPPVNVSCN IFINSFGSIA ETTMDYRVN IFLRQQWNDP RLAYNEYPDD SLDLDPSMLD SIWKPDLFFA NEKGAHFHEI TTDNKLLRIS RNGNVLYSIR I TLTLACPM ...String:
MYRFNTLRLY LWETIVFFSL AASKEAEAAR SASKPMSPSD FLDKLMGRTS GYDARIRPNF KGPPVNVSCN IFINSFGSIA ETTMDYRVN IFLRQQWNDP RLAYNEYPDD SLDLDPSMLD SIWKPDLFFA NEKGAHFHEI TTDNKLLRIS RNGNVLYSIR I TLTLACPM DLKNFPMDVQ TCIMQLESFG YTMNDLIFEW QEQGAVQVAD GLTLPQFILK EEKDLRYCTK HYNTGKFTCI EA RFHLERQ MGYYLIQMYI PSLLIVILSW ISFWINMDAA PARVGLGITT VLTMTTQSSG SRASLPKVSY VKAIDIWMAV CLL FVFSAL LEYAAVNFVS RQHKELLRFR RKRRHHKSPM LNLFQEDEAG EGRFNFSAYG MGPACLQAKD GISVKGANNT TTNP PPAPS KSPEEMRKLF IQRAKKIDKI SRIGFPMAFL IFNMFYWIIY KIVRREDVHN Q

UniProtKB: Glycine receptor alpha 1

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Macromolecule #7: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 7 / Number of copies: 4 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Macromolecule #8: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.05 mg/mL
BufferpH: 8
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: 28.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 129772
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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