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- EMDB-23913: Cryo-EM reveals partially and fully assembled native glycine rece... -

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Basic information

Entry
Database: EMDB / ID: EMD-23913
TitleCryo-EM reveals partially and fully assembled native glycine receptors,heteromeric pentamer
Map dataunsharpened map
Sample
  • Complex: Native heteromeric glycine receptor bound with 3D1 fab
    • Complex: Native heteromeric glycine receptor
      • Protein or peptide: x 2 types
    • Complex: 3D1 fab
      • Protein or peptide: x 2 types
  • Ligand: x 11 types
Keywordsglycine receptor / ion channel / heteromeric pentamer / 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 / synaptic transmission, glycinergic / positive regulation of acrosome reaction / acrosome reaction / glycine-gated chloride channel complex / gamma-aminobutyric acid receptor clustering / neuromuscular process controlling posture / extracellularly glycine-gated ion channel activity ...Neurotransmitter receptors and postsynaptic signal transmission / taurine binding / negative regulation of transmission of nerve impulse / synaptic transmission, glycinergic / positive regulation of acrosome reaction / acrosome reaction / glycine-gated chloride channel complex / gamma-aminobutyric acid receptor clustering / neuromuscular process controlling posture / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / regulation of respiratory gaseous exchange by nervous system process / inhibitory synapse / excitatory extracellular ligand-gated monoatomic ion channel activity / glycinergic synapse / adult walking behavior / inhibitory postsynaptic potential / glycine binding / cellular response to zinc ion / startle response / cellular response to ethanol / neuropeptide signaling pathway / chloride channel complex / neuronal action potential / monoatomic ion transport / visual perception / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / muscle contraction / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / GABA-ergic synapse / transmembrane signaling receptor activity / nervous system development / perikaryon / chemical synaptic transmission / postsynaptic membrane / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / zinc 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 ...: / 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 speciesSus scrofa (pig) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mly
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7mly
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23913.png

Downloads & links

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Map

FileDownload / File: emd_23913.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396.48 Å		0.83 Å/pix.
x 480 pix.
= 396.48 Å		0.83 Å/pix.
x 480 pix.
= 396.48 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: 0.133 / Movie #1: 0.17
Minimum - Maximum-0.3073197 - 0.96997994
Average (Standard dev.)0.00041566548 (±0.024008492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8260.8260.826
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z396.480396.480396.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.3070.9700.000

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Supplemental data

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Additional map: Localscale sharpened map

Fileemd_23913_additional_1.map
AnnotationLocalscale sharpened 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 : Native heteromeric glycine receptor bound with 3D1 fab

EntireName: Native heteromeric glycine receptor bound with 3D1 fab
Components
  • Complex: Native heteromeric glycine receptor bound with 3D1 fab
    • Complex: Native heteromeric glycine receptor
      • Protein or peptide: Glycine receptor alpha 1
      • Protein or peptide: Glycine receptor beta
    • Complex: 3D1 fab
      • Protein or peptide: 3D1 Fab Light Chain
      • Protein or peptide: 3D1 Fab Heavy Chain
  • Ligand: HEPTANE
  • Ligand: nonane
  • Ligand: PENTANE
  • Ligand: PENTADECANE
  • Ligand: DECANE
  • Ligand: N-BUTANE
  • Ligand: GLYCINE
  • Ligand: DODECANE
  • Ligand: N-OCTANE
  • Ligand: HEXANE
  • Ligand: UNDECANE

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

SupramoleculeName: Native heteromeric glycine receptor bound with 3D1 fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 500 KDa

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Supramolecule #2: Native heteromeric glycine receptor

SupramoleculeName: Native heteromeric glycine receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
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: 51.507523 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 KI

UniProtKB: Glycine receptor alpha 1

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Macromolecule #4: Glycine receptor beta

MacromoleculeName: Glycine receptor beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 56.200996 KDa
SequenceString: MKFLLAVAFF ILISLWVEEA YSKEKSSKKG KGKKKQYLCP SQQSAEDLAR VPANSTSNIL NRLLVSYDPR IRPNFKGIPV DVVVNIFIN SFGSIQETTM DYRVNIFLRQ KWNDPRLKLP SDFRGSDALT VDPTMYKCLW KPDLFFANEK SANFHDVTQE N ILLFIFRD ...String:
MKFLLAVAFF ILISLWVEEA YSKEKSSKKG KGKKKQYLCP SQQSAEDLAR VPANSTSNIL NRLLVSYDPR IRPNFKGIPV DVVVNIFIN SFGSIQETTM DYRVNIFLRQ KWNDPRLKLP SDFRGSDALT VDPTMYKCLW KPDLFFANEK SANFHDVTQE N ILLFIFRD GDVLVSMRLS ITLSCPLDLT LFPMDTQRCK MQLESFGYTT DDLRFIWQSG DPVQLEKIAL PQFDIKKEDI EY GNCTKYY KGTGYYTCVE VIFTLRRQVG FYMMGVYAPT LLIVVLSWLS FWINPDASAA RVPLGIFSVL SLASECTTLA AEL PKVSYV KALDVWLIAC LLFGFASLVE YAVVQVMLNN PKRVEAEKAR IAKAEQADGK GANAVKKNTV NGTGTPVHIS TLQV GETRC KKVCTSKSDL RSNDFSIVGS LPRDFELSNY DCYGKPIEVN NGLGKSQAKN NKKPPPAKPV IPTAAKRIDL YARAL FPFC FLFFNVIYWS IYL

UniProtKB: Glycine receptor subunit beta

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Macromolecule #9: HEPTANE

MacromoleculeName: HEPTANE / type: ligand / ID: 9 / Number of copies: 9 / Formula: HP6
Molecular weightTheoretical: 100.202 Da
Chemical component information

ChemComp-HP6:
HEPTANE

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Macromolecule #10: nonane

MacromoleculeName: nonane / type: ligand / ID: 10 / Number of copies: 3 / Formula: DD9
Molecular weightTheoretical: 128.255 Da
Chemical component information

ChemComp-DD9:
nonane

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Macromolecule #11: PENTANE

MacromoleculeName: PENTANE / type: ligand / ID: 11 / Number of copies: 10 / Formula: LNK
Molecular weightTheoretical: 72.149 Da
Chemical component information

ChemComp-LNK:
PENTANE

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Macromolecule #12: PENTADECANE

MacromoleculeName: PENTADECANE / type: ligand / ID: 12 / Number of copies: 1 / Formula: MYS
Molecular weightTheoretical: 212.415 Da
Chemical component information

ChemComp-MYS:
PENTADECANE

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Macromolecule #13: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 13 / Number of copies: 1 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #14: N-BUTANE

MacromoleculeName: N-BUTANE / type: ligand / ID: 14 / Number of copies: 9 / Formula: NBU
Molecular weightTheoretical: 58.122 Da
Chemical component information

ChemComp-NBU:
N-BUTANE

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Macromolecule #15: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 15 / Number of copies: 5 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #16: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 16 / Number of copies: 2 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #17: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 17 / Number of copies: 4 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #18: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 18 / Number of copies: 3 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #19: UNDECANE

MacromoleculeName: UNDECANE / type: ligand / ID: 19 / Number of copies: 1 / Formula: UND
Molecular weightTheoretical: 156.308 Da
Chemical component information

ChemComp-UND:
UNDECANE

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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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 527075
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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