+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21534 | |||||||||
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Title | CryoEM Structure of GABAB1b Homodimer | |||||||||
Map data | GABAB1b Homodimer Focused Refinement VFT and Linker | |||||||||
Sample |
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Function / homology | Function and homology information G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / negative regulation of gamma-aminobutyric acid secretion / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion ...G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / negative regulation of gamma-aminobutyric acid secretion / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion / positive regulation of growth hormone secretion / extracellular matrix protein binding / Class C/3 (Metabotropic glutamate/pheromone receptors) / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / positive regulation of glutamate secretion / negative regulation of synaptic transmission / axolemma / GABA-ergic synapse / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / response to nicotine / Schaffer collateral - CA1 synapse / mitochondrial membrane / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / osteoblast differentiation / synaptic vesicle / presynaptic membrane / G alpha (i) signalling events / postsynaptic membrane / response to ethanol / dendritic spine / protein heterodimerization activity / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Papasergi-Scott MM / Robertson MJ / Skiniotis G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2020 Title: Structures of metabotropic GABA receptor. Authors: Makaía M Papasergi-Scott / Michael J Robertson / Alpay B Seven / Ouliana Panova / Jesper M Mathiesen / Georgios Skiniotis / Abstract: Stimulation of the metabotropic GABA receptor by γ-aminobutyric acid (GABA) results in prolonged inhibition of neurotransmission, which is central to brain physiology. GABA belongs to family C of ...Stimulation of the metabotropic GABA receptor by γ-aminobutyric acid (GABA) results in prolonged inhibition of neurotransmission, which is central to brain physiology. GABA belongs to family C of the G-protein-coupled receptors, which operate as dimers to transform synaptic neurotransmitter signals into a cellular response through the binding and activation of heterotrimeric G proteins. However, GABA is unique in its function as an obligate heterodimer in which agonist binding and G-protein activation take place on distinct subunits. Here we present cryo-electron microscopy structures of heterodimeric and homodimeric full-length GABA receptors. Complemented by cellular signalling assays and atomistic simulations, these structures reveal that extracellular loop 2 (ECL2) of GABA has an essential role in relaying structural transitions by ordering the linker that connects the extracellular ligand-binding domain to the transmembrane region. Furthermore, the ECL2 of each of the subunits of GABA caps and interacts with the hydrophilic head of a phospholipid that occupies the extracellular half of the transmembrane domain, thereby providing a potentially crucial link between ligand binding and the receptor core that engages G proteins. These results provide a starting framework through which to decipher the mechanistic modes of signal transduction mediated by GABA dimers, and have important implications for rational drug design that targets these receptors. | |||||||||
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_21534.map.gz | 9.2 MB | EMDB map data format | |
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Header (meta data) | emd-21534-v30.xml emd-21534.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_21534.png | 124.6 KB | ||
Others | emd_21534_additional.map.gz | 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21534 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21534 | HTTPS FTP |
-Validation report
Summary document | emd_21534_validation.pdf.gz | 334.4 KB | Display | EMDB validaton report |
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Full document | emd_21534_full_validation.pdf.gz | 334 KB | Display | |
Data in XML | emd_21534_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_21534_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21534 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21534 | HTTPS FTP |
-Related structure data
Related structure data | 6w2yMC 6w2xC 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_21534.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | GABAB1b Homodimer Focused Refinement VFT and Linker | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: GABAB1b Homodimer Focused Refinement VFT and Linker
File | emd_21534_additional.map | ||||||||||||
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Annotation | GABAB1b Homodimer Focused Refinement VFT and Linker | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GABAB1b Homodimer
Entire | Name: GABAB1b Homodimer |
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Components |
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-Supramolecule #1: GABAB1b Homodimer
Supramolecule | Name: GABAB1b Homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Gamma-aminobutyric acid type B receptor subunit 1
Macromolecule | Name: Gamma-aminobutyric acid type B receptor subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 94.17357 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DYKDDDDKSH SPHLPRPHSR VPPHPSSERR AVYIGALFPM SGGWPGGQAC QPAVEMALED VNSRRDILPD YELKLIHHDS KCDPGQATK YLYELLYNDP IKIILMPGCS SVSTLVAEAA RMWNLIVLSY GSSSPALSNR QRFPTFFRTH PSATLHNPTR V KLFEKWGW ...String: DYKDDDDKSH SPHLPRPHSR VPPHPSSERR AVYIGALFPM SGGWPGGQAC QPAVEMALED VNSRRDILPD YELKLIHHDS KCDPGQATK YLYELLYNDP IKIILMPGCS SVSTLVAEAA RMWNLIVLSY GSSSPALSNR QRFPTFFRTH PSATLHNPTR V KLFEKWGW KKIATIQQTT EVFTSTLDDL EERVKEAGIE ITFRQSFFSD PAVPVKNLKR QDARIIVGLF YETEARKVFC EV YKERLFG KKYVWFLIGW YADNWFKIYD PSINCTVDEM TEAVEGHITT EIVMLNPANT RSISNMTSQE FVEKLTKRLK RHP EETGGF QEAPLAYDAI WALALALNKT SGGGGRSGVR LEDFNYNNQT ITDQIYRAMN SSSFEGVSGH VVFDASGSRM AWTL IEQLQ GGSYKKIGYY DSTKDDLSWS KTDKWIGGSP PADQTLVIKT FRFLSQKLFI SVSVLSSLGI VLAVVCLSFN IYNSH VRYI QNSQPNLNNL TAVGCSLALA AVFPLGLDGY HIGRNQFPFV CQARLWLLGL GFSLGYGSMF TKIWWVHTVF TKKEEK KEW RKTLEPWKLY ATVGLLVGMD VLTLAIWQIV DPLHRTIETF AKEEPKEDID VSILPQLEHC SSRKMNTWLG IFYGYKG LL LLLGIFLAYE TKSVSTEKIN DHRAVGMAIY NVAVLCLITA PVTMILSSQQ DAAFAFASLA IVFSSYITLV VLFVPKMR R LITRGEWQSE AQDTMKTGSS TNNNEEEKSR LLEKENRELE KIIAEKEERV SELRHQLQSR QQLRSRRHPP TPPEPSGGL PRGPPEPPDR LSCDGSRVHL LYKHHHHHH |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadeca...
Macromolecule | Name: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate type: ligand / ID: 5 / Number of copies: 2 / Formula: L9Q |
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Molecular weight | Theoretical: 746.05 Da |
Chemical component information | ChemComp-L9Q: |
-Macromolecule #6: [(2~{S})-3-[[(1~{S})-1-(3,4-dichlorophenyl)ethyl]amino]-2-oxidany...
Macromolecule | Name: [(2~{S})-3-[[(1~{S})-1-(3,4-dichlorophenyl)ethyl]amino]-2-oxidanyl-propyl]-(phenylmethyl)phosphinic acid type: ligand / ID: 6 / Number of copies: 2 / Formula: SGG |
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Molecular weight | Theoretical: 402.252 Da |
Chemical component information | ChemComp-SGG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.0 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 8.0 sec. / Average electron dose: 49.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |