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- PDB-3jaf: Structure of alpha-1 glycine receptor by single particle electron... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jaf | |||||||||
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Title | Structure of alpha-1 glycine receptor by single particle electron cryo-microscopy, glycine/ivermectin-bound state | |||||||||
![]() | Glycine receptor subunit alphaZ1 | |||||||||
![]() | SIGNALING PROTEIN / cys loop receptor / alpha-1 glycine receptor / glycine / ivermectin | |||||||||
Function / homology | ![]() Neurotransmitter receptors and postsynaptic signal transmission / transmitter-gated monoatomic ion channel activity / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding / chloride channel complex ...Neurotransmitter receptors and postsynaptic signal transmission / transmitter-gated monoatomic ion channel activity / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding / chloride channel complex / ligand-gated monoatomic ion channel activity / transmembrane transporter complex / response to amino acid / monoatomic ion transport / chloride transmembrane transport / cellular response to amino acid stimulus / central nervous system development / transmembrane signaling receptor activity / postsynaptic membrane / perikaryon / neuron projection / synapse / dendrite / zinc ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Du, J. / Lu, W. / Wu, S.P. / Cheng, Y.F. / Gouaux, E. | |||||||||
![]() | ![]() Title: Glycine receptor mechanism elucidated by electron cryo-microscopy. Authors: Juan Du / Wei Lü / Shenping Wu / Yifan Cheng / Eric Gouaux / ![]() Abstract: The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders, including autism and hyperekplexia. ...The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders, including autism and hyperekplexia. Understanding of molecular mechanisms and pharmacology of glycine receptors has been hindered by a lack of high-resolution structures. Here we report electron cryo-microscopy structures of the zebrafish α1 GlyR with strychnine, glycine, or glycine and ivermectin (glycine/ivermectin). Strychnine arrests the receptor in an antagonist-bound closed ion channel state, glycine stabilizes the receptor in an agonist-bound open channel state, and the glycine/ivermectin complex adopts a potentially desensitized or partially open state. Relative to the glycine-bound state, strychnine expands the agonist-binding pocket via outward movement of the C loop, promotes rearrangement of the extracellular and transmembrane domain 'wrist' interface, and leads to rotation of the transmembrane domain towards the pore axis, occluding the ion conduction pathway. These structures illuminate the GlyR mechanism and define a rubric to interpret structures of Cys-loop receptors. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 309.2 KB | Display | ![]() |
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PDB format | ![]() | 259.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 59.2 KB | Display | |
Data in CIF | ![]() | 77.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6346MC ![]() 6344C ![]() 6345C ![]() 3jadC ![]() 3jaeC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 39223.539 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-IVM / ( |
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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: zebra fish alpha-1 glycine receptor bound with glycine/ivermectin Type: COMPLEX / Details: pentamer |
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Molecular weight | Value: 0.2 MDa / Experimental value: NO |
Buffer solution | Name: 150 mM NaCl, 20 mM Tris-HCl, 1 mM C12M, 10 mM glycine, 5 uM ivermectin pH: 8 Details: 150 mM NaCl, 20 mM Tris-HCl, 1 mM C12M, 10 mM glycine, 5 uM ivermectin |
Specimen | Conc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 200 mesh copper 1.2/1.3 Quantifoil carbon grid |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 % Details: Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK III). Method: Blot for 3.5 seconds before plunging. |
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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 / Date: Oct 6, 2014 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -3000 nm / Nominal defocus min: -1500 nm / Cs: 0.01 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 46 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
EM imaging optics | Energyfilter name: GIF |
Image scans | Num. digital images: 2489 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: each particle | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56957 / Nominal pixel size: 1.04 Å / Actual pixel size: 1.04 Å Details: Particle picking, 2D classification, 3D classification, refinement, and reconstruction were done using Relion. Movies were aligned using motioncorr. (Single particle--Applied symmetry: C5) Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: REFINEMENT PROTOCOL--rigid body DETAILS--The model (3RHW) was fit into the density map using UCSF Chimera. Further de novo model building was done using COOT. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Resolution: 3.801→49.94 Å / SU ML: 0.83 / σ(F): 10 / Phase error: 37.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.48 Å2 / Biso mean: 76.3531 Å2 / Biso min: 41.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.801→49.94 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: ELECTRON MICROSCOPY / Total num. of bins used: 30
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