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- PDB-8dn3: Cryo-EM structure of human Glycine Receptor alpha1-beta heteromer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dn3 | ||||||
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Title | Cryo-EM structure of human Glycine Receptor alpha1-beta heteromer, apo state | ||||||
![]() | (Glycine receptor subunit ...) x 2 | ||||||
![]() | MEMBRANE PROTEIN / glycine receptor subunit alpha-1 / glycine receptor subunit beta / Green fluorescent protein | ||||||
Function / homology | ![]() taurine binding / glycine-gated chloride channel complex / negative regulation of transmission of nerve impulse / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / positive regulation of acrosome reaction / synaptic transmission, glycinergic / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / response to alcohol ...taurine binding / glycine-gated chloride channel complex / negative regulation of transmission of nerve impulse / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / positive regulation of acrosome reaction / synaptic transmission, glycinergic / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / response to alcohol / neuromuscular process controlling posture / inhibitory synapse / extracellularly glycine-gated ion channel activity / 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 / chloride transport / cellular response to zinc ion / neurotransmitter receptor activity / glycine binding / startle response / chloride channel complex / neuropeptide signaling pathway / neuronal action potential / transmembrane transporter complex / GABA-ergic synapse / monoatomic ion transport / muscle contraction / chloride transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / visual perception / bioluminescence / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / generation of precursor metabolites and energy / cellular response to amino acid stimulus / transmembrane signaling receptor activity / nervous system development / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron projection / external side of plasma membrane / intracellular membrane-bounded organelle / neuronal cell body / synapse / dendrite / protein-containing complex binding / zinc ion binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å | ||||||
![]() | Liu, X. / Wang, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Asymmetric gating of a human hetero-pentameric glycine receptor. Authors: Xiaofen Liu / Weiwei Wang / ![]() Abstract: Hetero-pentameric Cys-loop receptors constitute a major type of neurotransmitter receptors that enable signal transmission and processing in the nervous system. Despite intense investigations into ...Hetero-pentameric Cys-loop receptors constitute a major type of neurotransmitter receptors that enable signal transmission and processing in the nervous system. Despite intense investigations into their working mechanism and pharmaceutical potentials, how neurotransmitters activate these receptors remains unclear due to the lack of high-resolution structural information in the activated open state. Here we report near-atomic resolution structures resolved in digitonin consistent with all principle functional states of the human α1β GlyR, which is a major Cys-loop receptor that mediates inhibitory neurotransmission in the central nervous system of adults. Glycine binding induces cooperative and symmetric structural rearrangements in the neurotransmitter-binding extracellular domain but asymmetrical pore dilation in the transmembrane domain. Symmetric response in the extracellular domain is consistent with electrophysiological data showing cooperative glycine activation and contribution from both α1 and β subunits. A set of functionally essential but differentially charged amino acid residues in the transmembrane domain of the α1 and β subunits explains asymmetric activation. These findings provide a foundation for understanding how the gating of the Cys-loop receptor family members diverges to accommodate specific physiological environments. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 351.4 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 27553MC ![]() 8dn2C ![]() 8dn4C ![]() 8dn5C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Glycine receptor subunit ... , 2 types, 5 molecules DABCE
#1: Protein | Mass: 42421.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Derived by substitution of M3/M4 loop (residues R316-P381) s by GSSG peptide. Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 76584.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: GLRB, GFP / Production host: ![]() References: UniProt: P48167, UniProt: P42212, UniProt: A0A2K6CAQ3 |
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-Sugars , 1 types, 5 molecules ![](data/chem/img/NAG.gif)
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 56 molecules ![](data/chem/img/HEX.gif)
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#4: Chemical | ChemComp-HEX / #5: Chemical | ChemComp-UND / #6: Chemical | ChemComp-DD9 / #7: Chemical | ChemComp-NBU / #8: Chemical | ChemComp-HP6 / #9: Chemical | ChemComp-D10 / | #10: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: heteromeric glycine receptor alpha-1 and beta, apo state Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.24 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Electron dose: 69.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29850 / Symmetry type: POINT |
Atomic model building | Space: REAL |
Atomic model building | PDB-ID: 7MLY Accession code: 7MLY / Source name: PDB / Type: experimental model |
Refinement | Cross valid method: NONE |