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Yorodumi- EMDB-8923: Cryo-EM structure of the benzodiazepine-sensitive alpha1-beta1-ga... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8923 | |||||||||
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Title | Cryo-EM structure of the benzodiazepine-sensitive alpha1-beta1-gamma2 heterotrimeric GABAA receptor in complex with GABA | |||||||||
Map data | Benzodiazepine-sensitive alpha1-beta1-gamma2 heterotrimeric GABAA receptor in complex with GABA | |||||||||
Sample |
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Keywords | Neurotransmission / GABA Receptors / GABA / Cys Loop Receptors / Ion Channel / MEMBRANE PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Phulera S / Zhu H | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8923.map.gz | 393 MB | EMDB map data format | |
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Header (meta data) | emd-8923-v30.xml emd-8923.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_8923.png | 51.6 KB | ||
Filedesc metadata | emd-8923.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8923 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8923 | HTTPS FTP |
-Validation report
Summary document | emd_8923_validation.pdf.gz | 573.4 KB | Display | EMDB validaton report |
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Full document | emd_8923_full_validation.pdf.gz | 572.9 KB | Display | |
Data in XML | emd_8923_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_8923_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8923 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8923 | HTTPS FTP |
-Related structure data
Related structure data | 6dw1MC 8922C 6dw0C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8923.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Benzodiazepine-sensitive alpha1-beta1-gamma2 heterotrimeric GABAA receptor in complex with GABA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.649 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Triheteromeric alpha1-beta1-gamma2 GABAA receptor
Entire | Name: Triheteromeric alpha1-beta1-gamma2 GABAA receptor |
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Components |
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-Supramolecule #1: Triheteromeric alpha1-beta1-gamma2 GABAA receptor
Supramolecule | Name: Triheteromeric alpha1-beta1-gamma2 GABAA receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: In complex with alpha1 specific Fab |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Macromolecule #1: Gamma-aminobutyric acid receptor subunit gamma-2
Macromolecule | Name: Gamma-aminobutyric acid receptor subunit gamma-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 56.894949 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSSPNTWSTG STVYSPVFSQ KMTLWILLLL SLYPGFTSQK SDDDYEDYAS NKTWVLTPKV PEGDVTVILN NLLEGYDNKL RPDIGVKPT LIHTDMYVNS IGPVNAINME YTIDIFFAQT WYDRRLKFNS TIKVLRLNSN MVGKIWIPDT FFRNSKKADA H WITTPNRM ...String: MSSPNTWSTG STVYSPVFSQ KMTLWILLLL SLYPGFTSQK SDDDYEDYAS NKTWVLTPKV PEGDVTVILN NLLEGYDNKL RPDIGVKPT LIHTDMYVNS IGPVNAINME YTIDIFFAQT WYDRRLKFNS TIKVLRLNSN MVGKIWIPDT FFRNSKKADA H WITTPNRM LRIWNDGRVL YTLRLTIDAE CQLQLHNFPM DEHSCPLEFS SYGYPREEIV YQWKRSSVEV GDTRSWRLYQ FS FVGLRNT TEVVKTTSGD YVVMSVYFDL SRRMGYFTIQ TYIPCTLIVV LSWVSFWINK DAVPARTSLG ITTVLTMTTL STI ARKSLP KVSYVTAMDL FVSVCFIFVF SALVEYGTLH YFVSNRKPSK DKDKKKKNPA PTIDIRPRSA TIQMNNATHL QERD EEYGY ECLDGKDCAS FFCCFEDCRT GAWRHGRIHI RIAKMDSYAR IFFPTAFCLF NLVYWVSYLY LLVPRGSRHH HHHHH HTET SQVAPA UniProtKB: Gamma-aminobutyric acid receptor subunit gamma-2 |
-Macromolecule #2: Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyr...
Macromolecule | Name: Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1 type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 46.267105 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKKSRGLSDY LWAWTLILST LSGRSYGQPS QDELKDNTTV FTRILDRLLD GYDNRLRPGL GERVTEVKTD IFVTSFGPVS DHDMEYTID VFFRQSWKDE RLKFKGPMTV LRLNNLMASK IWTPDTFFHN GKKSVAHNMT MPNKLLRITE DGTLLYTMRL T VRAECPMH ...String: MKKSRGLSDY LWAWTLILST LSGRSYGQPS QDELKDNTTV FTRILDRLLD GYDNRLRPGL GERVTEVKTD IFVTSFGPVS DHDMEYTID VFFRQSWKDE RLKFKGPMTV LRLNNLMASK IWTPDTFFHN GKKSVAHNMT MPNKLLRITE DGTLLYTMRL T VRAECPMH LEDFPMDAHA CPLKFGSYAY TRAEVVYEWT REPARSVVVA EDGSRLNQYD LLGQTVDSGI VQSSTGEYVV MT THFHLKR KIGYFVIQTY LPCIMTVILS QVSFWLNRES VPARTVFGVT TVLTMTTLSI SARNSLPKVA YATAMDWFIA VCY AFVFSA LIEFATVNYF TKRGTKKTFN SVSKIDRLSR IAFPLLFGIF NLVYWATYLN REPQLKAPTP HQLVPRGSHH HHHH HH UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-1, Gamma-aminobutyric acid receptor subunit alpha-1 |
-Macromolecule #3: Gamma-aminobutyric acid receptor subunit beta-1,Gamma-aminobutyri...
Macromolecule | Name: Gamma-aminobutyric acid receptor subunit beta-1,Gamma-aminobutyric acid receptor subunit beta-1 type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 44.333012 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MWTVQNRESL GLLSFPVMVA MVCCAHSSNE PSNMSYVKET VDRLLKGYDI RLRPDFGGPP VDVGMRIDVA SIDMVSEVNM DYTLTMYFQ QSWKDKRLSY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY ...String: MWTVQNRESL GLLSFPVMVA MVCCAHSSNE PSNMSYVKET VDRLLKGYDI RLRPDFGGPP VDVGMRIDVA SIDMVSEVNM DYTLTMYFQ QSWKDKRLSY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY PLDEQNCTLE IESYGYTTDD IEFYWNGGEG AVTGVNKIEL PQFSIVDYKM VSKKVEFTTG AYPRLSLSFR LK RNIGYFI LQTYMPSTLI TILSWVSFWI NYDASAARVA LGITTVLTMT TISTHLRETL PKIPYVKAID IYLMGCFVFV FLA LLEYAF VNYIFFGGTI PDLTDVNSID KWSRMFFPIT FSLFNVVYWL YYVHLVPRGS HHHHHHHH UniProtKB: Gamma-aminobutyric acid receptor subunit beta-1, Gamma-aminobutyric acid receptor subunit beta-1 |
-Macromolecule #8: GAMMA-AMINO-BUTANOIC ACID
Macromolecule | Name: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 8 / Number of copies: 3 / Formula: ABU |
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Molecular weight | Theoretical: 103.12 Da |
Chemical component information | ChemComp-ABU: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL | |||||||||||||||
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Buffer | pH: 7.3 Component:
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Grid | Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Details: unspecified | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1391 / Average exposure time: 40.0 sec. / Average electron dose: 37.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.2 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: cryoSPARC was used to generate the initial model |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 68499 |
Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC / Details: Stochastic Gradient Descent |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: 0.74 |
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Output model | PDB-6dw1: |