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Yorodumi- PDB-7tu9: Alpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tu9 | ||||||
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Title | Alpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State | ||||||
Components | (Glycine receptor ...) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / Glycine / Ion Channel / Strychnine | ||||||
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 Å | ||||||
Authors | Gibbs, E. / Kumar, A. / Chakrapani, S. | ||||||
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 | 7tu9.cif.gz | 330.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tu9.ent.gz | 265.3 KB | Display | PDB format |
PDBx/mmJSON format | 7tu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tu9_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7tu9_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7tu9_validation.xml.gz | 63.9 KB | Display | |
Data in CIF | 7tu9_validation.cif.gz | 91 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/7tu9 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/7tu9 | HTTPS FTP |
-Related structure data
Related structure data | 26130MC 7tviC 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
-Glycine receptor ... , 2 types, 5 molecules ADCBE
#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 |
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-Sugars , 1 types, 6 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 25 molecules
#4: Chemical | ChemComp-PIO / [( #5: Chemical | ChemComp-PX4 / #6: Chemical | ChemComp-SY9 / |
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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 |
-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: 0.25 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 | Conc.: 0.1 mg/ml / 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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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-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: 200000 | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131757 / Details: Non-Uniform Refinement Cryosparc / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Refine LS restraints |
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