+Open data
-Basic information
Entry | Database: PDB / ID: 7tvi | ||||||
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Title | Alpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Glycine / Ion Channel / Ligand-Gated / Receptor | ||||||
Function / homology | Function and homology information Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / cellular response to ethanol / cellular response to zinc ion / neurotransmitter receptor activity / regulation of neuron differentiation / glycine binding / chloride channel complex ...Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / cellular response to ethanol / cellular response to zinc ion / neurotransmitter receptor activity / regulation of neuron differentiation / glycine binding / chloride channel complex / ligand-gated monoatomic ion channel activity / transmembrane transporter complex / neuropeptide signaling pathway / response to amino acid / monoatomic ion transport / chloride transmembrane transport / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / protein localization / transmembrane signaling receptor activity / postsynaptic membrane / perikaryon / neuron projection / synapse / dendrite / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Gibbs, E. / Chakrapani, S. / Kumar, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Conformational transitions and allosteric modulation in a heteromeric glycine receptor Authors: Gibbs, E. / Klemm, E. / Seiferth, D. / Kumar, A. / Ilca, S.L. / Biggin, P.C. / Chakrapani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tvi.cif.gz | 313.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tvi.ent.gz | 253.2 KB | Display | PDB format |
PDBx/mmJSON format | 7tvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tvi_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7tvi_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7tvi_validation.xml.gz | 60.4 KB | Display | |
Data in CIF | 7tvi_validation.cif.gz | 88.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/7tvi ftp://data.pdbj.org/pub/pdb/validation_reports/tv/7tvi | HTTPS FTP |
-Related structure data
Related structure data | 26141MC 7tu9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 52537.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: glra1 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: O93430 #2: Protein | | Mass: 65820.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: glrbb, glrb2 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q6DC22 #3: Chemical | ChemComp-GLY / #4: Sugar | ChemComp-NAG / 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 |
-Sample preparation
Component | Name: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: .25 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Danio rerio (zebrafish) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Single Particle | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||
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EM imaging | Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: FEI TITAN KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm / Specimen-ID: 1
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Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 350000 | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205704 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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