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- EMDB-29733: Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-b... -
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Open data
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Basic information
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Title | Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA and allopregnanolone | |||||||||
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![]() | ligand-gated ion channel / cys-loop receptor / neurotransmitter receptor / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / diazepam binding / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / cellular response to histamine / inner ear receptor cell development / GABA-A receptor activity / GABA-gated chloride ion channel activity ...GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / diazepam binding / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / cellular response to histamine / inner ear receptor cell development / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / innervation / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / neurotransmitter receptor activity / adult behavior / cochlea development / chloride channel activity / chloride channel complex / transmembrane transporter complex / GABA-ergic synapse / neuron development / regulation of postsynaptic membrane potential / 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 / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / cytoplasmic vesicle / chemical synaptic transmission / postsynapse / neuron projection / axon / glutamatergic synapse / synapse / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | |||||||||
![]() | Sun C / Gouaux E | |||||||||
Funding support | ![]()
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![]() | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / ![]() ![]() ![]() Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 85.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.3 KB 25.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.9 KB | Display | ![]() |
Images | ![]() | 186.8 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 8.3 KB | ||
Others | ![]() ![]() | 165.3 MB 165.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g4xMC ![]() 8foiC ![]() 8g4nC ![]() 8g4oC ![]() 8g5fC ![]() 8g5gC ![]() 8g5hC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.831 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
+Entire : Native GABAA Receptor isolated from mouse brain containing one al...
+Supramolecule #1: Native GABAA Receptor isolated from mouse brain containing one al...
+Macromolecule #1: Gamma-aminobutyric acid receptor subunit alpha-1
+Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-2
+Macromolecule #3: Gamma-aminobutyric acid receptor subunit gamma-2
+Macromolecule #4: Heavy Chain of 8E3 Fab
+Macromolecule #5: Light Chain of 8E3 Fab
+Macromolecule #6: Gamma-aminobutyric acid receptor subunit alpha-3
+Macromolecule #12: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...
+Macromolecule #13: GAMMA-AMINO-BUTANOIC ACID
+Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #15: allopregnanolone
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | This sample was monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8g4x: |