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- EMDB-23913: Cryo-EM reveals partially and fully assembled native glycine rece... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23913 | |||||||||
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Title | Cryo-EM reveals partially and fully assembled native glycine receptors,heteromeric pentamer | |||||||||
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![]() | glycine receptor / ion channel / heteromeric pentamer / MEMBRANE PROTEIN / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() 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 / regulation of respiratory gaseous exchange by nervous system process / extracellularly glycine-gated chloride channel activity / inhibitory synapse / 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 Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Zhu H / Gouaux E | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 209.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
Images | ![]() | 158.3 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() | 12.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 464.2 KB | Display | ![]() |
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Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mlyMC ![]() 7mluC ![]() 7mlvC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | unsharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Localscale sharpened map
File | emd_23913_additional_1.map | ||||||||||||
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Annotation | Localscale sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Native heteromeric glycine receptor bound with 3D1 fab
+Supramolecule #1: Native heteromeric glycine receptor bound with 3D1 fab
+Supramolecule #2: Native heteromeric glycine receptor
+Supramolecule #3: 3D1 fab
+Macromolecule #1: 3D1 Fab Light Chain
+Macromolecule #2: 3D1 Fab Heavy Chain
+Macromolecule #3: Glycine receptor alpha 1
+Macromolecule #4: Glycine receptor beta
+Macromolecule #9: HEPTANE
+Macromolecule #10: nonane
+Macromolecule #11: PENTANE
+Macromolecule #12: PENTADECANE
+Macromolecule #13: DECANE
+Macromolecule #14: N-BUTANE
+Macromolecule #15: GLYCINE
+Macromolecule #16: DODECANE
+Macromolecule #17: N-OCTANE
+Macromolecule #18: HEXANE
+Macromolecule #19: UNDECANE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 28.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 model | Type of model: NONE |
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Final reconstruction | Applied 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 assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |