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- EMDB-23910: 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-23910 | |||||||||
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Title | Cryo-EM reveals partially and fully assembled native glycine receptors,homomeric pentamer | |||||||||
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Function / homology | ![]() 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 / neuropeptide signaling pathway / neuronal action potential / 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 / postsynaptic membrane / perikaryon / 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: 4.1 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 | ![]() | 115.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.1 KB 16.1 KB | Display Display | ![]() |
Images | ![]() | 124.9 KB | ||
Others | ![]() | 9.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mluMC ![]() 7mlvC ![]() 7mlyC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Combined map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_23910_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 homomeric glycine receptor pentamer bound with 3D1 fab
Entire | Name: Native homomeric glycine receptor pentamer bound with 3D1 fab |
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Components |
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-Supramolecule #1: Native homomeric glycine receptor pentamer bound with 3D1 fab
Supramolecule | Name: Native homomeric glycine receptor pentamer bound with 3D1 fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Experimental: 500 KDa |
-Supramolecule #2: Native homomeric glycine receptor pentamer
Supramolecule | Name: Native homomeric glycine receptor pentamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: 3D1 fab
Supramolecule | Name: 3D1 fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 Details: The Fab fragments were cleaved from the monoclonal antibody that was expressed in the hybridoma |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: 3D1 Fab Light Chain
Macromolecule | Name: 3D1 Fab Light Chain / type: protein_or_peptide / ID: 1 Details: The protein was cleaved from the mAb that was expressed in the hybridoma Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.743124 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DIVMTQSHKF MSTSVGDRVS ITCKASQDVS TAVAWYQQKP GQSPKLLIYW ASTRHTGVPG RFTGSGSGTD YTLTISSVQA EDLSLYYCQ QHYSTPRTFG GGTKLEIK |
-Macromolecule #2: 3D1 Fab Heavy Chain
Macromolecule | Name: 3D1 Fab Heavy Chain / type: protein_or_peptide / ID: 2 Details: The protein was cleaved from the mAb that was expressed in the hybridoma Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.983512 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLQQSGAE LMKPGAAVKI SCKATGHTIS RYWIDWLKQR PGHGLEWIGE ILPGSGSTNY NEKFKGKATF TAEKSSNTAY MQLSSLTSE DSAVYYCAMG VRGNYFDYWG QGTTLTVSS |
-Macromolecule #3: Glycine receptor alpha 1
Macromolecule | Name: Glycine receptor alpha 1 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 52.64475 KDa |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-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
Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 20660 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |