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Yorodumi- PDB-6dw1: Cryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamm... -
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-Basic information
Entry | Database: PDB / ID: 6dw1 | ||||||||||||
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Title | Cryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamma2S tri-heteromeric GABAA receptor in complex with GABA (ECD map) | ||||||||||||
Components | (Gamma-aminobutyric acid receptor subunit ...) x 3 | ||||||||||||
Keywords | MEMBRANE PROTEIN / Neurotransmission / GABA Receptors / GABA / Cys Loop Receptors / Ion Channel | ||||||||||||
Function / homology | Function and homology information GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / diazepam binding / response to anesthetic / regulation of presynaptic membrane potential / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / cellular response to histamine ...GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / diazepam binding / response to anesthetic / regulation of presynaptic membrane potential / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / cellular response to histamine / response to auditory stimulus / monoatomic anion channel activity / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / GABA receptor binding / inhibitory synapse assembly / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / ovulation cycle / chloride transport / cellular response to zinc ion / neurotransmitter receptor activity / chloride channel activity / adult behavior / central nervous system neuron development / chloride channel complex / ligand-gated monoatomic ion channel activity / regulation of postsynaptic membrane potential / transmembrane transporter complex / GABA-ergic synapse / monoatomic ion transport / presynaptic active zone membrane / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / post-embryonic development / response to progesterone / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / Schaffer collateral - CA1 synapse / response to toxic substance / nuclear envelope / chemical synaptic transmission / response to ethanol / postsynapse / receptor complex / neuron projection / G protein-coupled receptor signaling pathway / axon / glutamatergic synapse / dendrite / synapse / cell surface / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Phulera, S. / Zhu, H. / Yu, J. / Yoshioka, C. / Gouaux, E. | ||||||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2018 Title: Cryo-EM structure of the benzodiazepine-sensitive α1β1γ2S tri-heteromeric GABA receptor in complex with GABA. Authors: Swastik Phulera / Hongtao Zhu / Jie Yu / Derek P Claxton / Nate Yoder / Craig Yoshioka / Eric Gouaux / Abstract: Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABA ...Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABA receptors are heteromeric assemblies sensitive to many important drugs, from sedatives to anesthetics and anticonvulsant agents, with mutant forms of GABA receptors implicated in multiple neurological diseases. Despite the profound importance of heteromeric GABA receptors in neuroscience and medicine, they have proven recalcitrant to structure determination. Here we present the structure of a tri-heteromeric α1β1γ2S GABA receptor in complex with GABA, determined by single particle cryo-EM at 3.1-3.8 Å resolution, elucidating molecular principles of receptor assembly and agonist binding. Remarkable N-linked glycosylation on the α1 subunit occludes the extracellular vestibule of the ion channel and is poised to modulate receptor assembly and perhaps ion channel gating. Our work provides a pathway to structural studies of heteromeric GABA receptors and a framework for rational design of novel therapeutic agents. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6dw1.cif.gz | 222.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dw1.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 6dw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dw1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6dw1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6dw1_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 6dw1_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/6dw1 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/6dw1 | HTTPS FTP |
-Related structure data
Related structure data | 8923MC 8922C 6dw0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Gamma-aminobutyric acid receptor subunit ... , 3 types, 5 molecules DCAEB
#1: Protein | Mass: 56894.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gabrg2 / Production host: Homo sapiens (human) / References: UniProt: P18508 | ||
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#2: Protein | Mass: 46267.105 Da / Num. of mol.: 2 / Fragment: residues 39-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gabra1, Gabra-1 / Production host: Homo sapiens (human) / References: UniProt: P62813 #3: Protein | Mass: 44333.012 Da / Num. of mol.: 2 / Fragment: residues 33-474 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gabrb1, Gabrb-1 / Production host: Homo sapiens (human) / References: UniProt: P15431 |
-Sugars , 4 types, 6 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 1 types, 3 molecules
#8: Chemical |
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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: Triheteromeric alpha1-beta1-gamma2 GABAA receptor / Type: COMPLEX / Details: In complex with alpha1 specific Fab / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Rattus norvegicus (Norway rat) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: TSA201 | |||||||||||||||||||||||||
Buffer solution | pH: 7.3 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: unspecified | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 magnification: 120000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 40 sec. / Electron dose: 37 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1391 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68499 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: 0.74 |