+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21685 | |||||||||||||||||||||
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Title | Structure of human GABA(B) receptor in an inactive state | |||||||||||||||||||||
Map data | Final composite map combining local reconstructions for the extracellular and transmembrane domains. Map was re-sampled in Chimera with pixel spacing 1.1 angstrom. | |||||||||||||||||||||
Sample |
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Keywords | G protein coupled receptor (GPCR) / GABA / GABA(B) receptor / Class C GPCR / Phospholipids / Inhibitory neurotransmission. / MEMBRANE PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information negative regulation of gamma-aminobutyric acid 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 / 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 ...negative regulation of gamma-aminobutyric acid 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 / 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 / GABA receptor complex / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / positive regulation of glutamate secretion / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / negative regulation of synaptic transmission / axolemma / GABA-ergic synapse / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / response to nicotine / mitochondrial membrane / Schaffer collateral - CA1 synapse / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / osteoblast differentiation / transmembrane signaling receptor activity / synaptic vesicle / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / neuron projection / G protein-coupled receptor signaling pathway / protein heterodimerization activity / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / extracellular space / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||
Authors | Park J / Fu Z / Frangaj A / Liu J / Mosyak L / Shen T / Slavkovich VN / Ray KM / Taura J / Cao B ...Park J / Fu Z / Frangaj A / Liu J / Mosyak L / Shen T / Slavkovich VN / Ray KM / Taura J / Cao B / Geng Y / Zuo H / Kou Y / Grassucci R / Chen S / Liu Z / Lin X / Williams JP / Rice WJ / Eng ET / Huang RK / Soni RK / Kloss B / Yu Z / Javitch JA / Hendrickson WA / Slesinger PA / Quick M / Graziano J / Yu H / Fiehn O / Clarke OB / Frank J / Fan QR | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Nature / Year: 2020 Title: Structure of human GABA receptor in an inactive state. Authors: Jinseo Park / Ziao Fu / Aurel Frangaj / Jonathan Liu / Lidia Mosyak / Tong Shen / Vesna N Slavkovich / Kimberly M Ray / Jaume Taura / Baohua Cao / Yong Geng / Hao Zuo / Yongjun Kou / Robert ...Authors: Jinseo Park / Ziao Fu / Aurel Frangaj / Jonathan Liu / Lidia Mosyak / Tong Shen / Vesna N Slavkovich / Kimberly M Ray / Jaume Taura / Baohua Cao / Yong Geng / Hao Zuo / Yongjun Kou / Robert Grassucci / Shaoxia Chen / Zheng Liu / Xin Lin / Justin P Williams / William J Rice / Edward T Eng / Rick K Huang / Rajesh K Soni / Brian Kloss / Zhiheng Yu / Jonathan A Javitch / Wayne A Hendrickson / Paul A Slesinger / Matthias Quick / Joseph Graziano / Hongtao Yu / Oliver Fiehn / Oliver B Clarke / Joachim Frank / Qing R Fan / Abstract: The human GABA receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction. A unique ...The human GABA receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction. A unique GPCR that is known to require heterodimerization for function, the GABA receptor has two subunits, GABA and GABA, that are structurally homologous but perform distinct and complementary functions. GABA recognizes orthosteric ligands, while GABA couples with G proteins. Each subunit is characterized by an extracellular Venus flytrap (VFT) module, a descending peptide linker, a seven-helix transmembrane domain and a cytoplasmic tail. Although the VFT heterodimer structure has been resolved, the structure of the full-length receptor and its transmembrane signalling mechanism remain unknown. Here we present a near full-length structure of the GABA receptor, captured in an inactive state by cryo-electron microscopy. Our structure reveals several ligands that preassociate with the receptor, including two large endogenous phospholipids that are embedded within the transmembrane domains to maintain receptor integrity and modulate receptor function. We also identify a previously unknown heterodimer interface between transmembrane helices 3 and 5 of both subunits, which serves as a signature of the inactive conformation. A unique 'intersubunit latch' within this transmembrane interface maintains the inactive state, and its disruption leads to constitutive receptor activity. | |||||||||||||||||||||
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_21685.map.gz | 45.8 MB | EMDB map data format | |
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Header (meta data) | emd-21685-v30.xml emd-21685.xml | 30.8 KB 30.8 KB | Display Display | EMDB header |
Images | emd_21685.png | 146.5 KB | ||
Filedesc metadata | emd-21685.cif.gz | 8.6 KB | ||
Others | emd_21685_additional_1.map.gz emd_21685_additional_2.map.gz emd_21685_additional_3.map.gz | 47.6 MB 47.9 MB 47.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21685 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21685 | HTTPS FTP |
-Validation report
Summary document | emd_21685_validation.pdf.gz | 474.2 KB | Display | EMDB validaton report |
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Full document | emd_21685_full_validation.pdf.gz | 473.8 KB | Display | |
Data in XML | emd_21685_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_21685_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21685 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21685 | HTTPS FTP |
-Related structure data
Related structure data | 6wivMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10410 (Title: Structure of human GABA(B) receptor in an inactive state Data size: 854.1 Data #1: Unaligned multi-frame micrographs of GABA(B) receptor in the inactive state [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21685.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final composite map combining local reconstructions for the extracellular and transmembrane domains. Map was re-sampled in Chimera with pixel spacing 1.1 angstrom. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Local reconstruction for the extracellular domain. Map was...
File | emd_21685_additional_1.map | ||||||||||||
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Annotation | Local reconstruction for the extracellular domain. Map was re-sampled in Chimera with pixel spacing 1.1 angstrom. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local reconstruction for the transmembrane domain. Map was...
File | emd_21685_additional_2.map | ||||||||||||
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Annotation | Local reconstruction for the transmembrane domain. Map was re-sampled in Chimera with pixel spacing 1.1 angstrom. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Global map without local refinement. Map was re-sampled...
File | emd_21685_additional_3.map | ||||||||||||
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Annotation | Global map without local refinement. Map was re-sampled in Chimera with pixel spacing 1.1 angstrom. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heterodimer human GABA(B) receptor composed of GABA(B1b) and GABA...
Entire | Name: Heterodimer human GABA(B) receptor composed of GABA(B1b) and GABA(B2) subunits. |
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Components |
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-Supramolecule #1: Heterodimer human GABA(B) receptor composed of GABA(B1b) and GABA...
Supramolecule | Name: Heterodimer human GABA(B) receptor composed of GABA(B1b) and GABA(B2) subunits. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 193 KDa |
-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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 91.585867 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGPGAPFARV GWPLPLLVVM AAGVAPVWAS HSPHLPRPHS RVPPHPSSER RAVYIGALFP MSGGWPGGQA CQPAVEMALE DVNSRRDIL PDYELKLIHH DSKCDPGQAT KYLYELLYND PIKIILMPGC SSVSTLVAEA ARMWNLIVLS YGSSSPALSN R QRFPTFFR ...String: MGPGAPFARV GWPLPLLVVM AAGVAPVWAS HSPHLPRPHS RVPPHPSSER RAVYIGALFP MSGGWPGGQA CQPAVEMALE DVNSRRDIL PDYELKLIHH DSKCDPGQAT KYLYELLYND PIKIILMPGC SSVSTLVAEA ARMWNLIVLS YGSSSPALSN R QRFPTFFR THPSATLHNP TRVKLFEKWG WKKIATIQQT TEVFTSTLDD LEERVKEAGI EITFRQSFFS DPAVPVKNLK RQ DARIIVG LFYETEARKV FCEVYKERLF GKKYVWFLIG WYADNWFKIY DPSINCTVDE MTEAVEGHIT TEIVMLNPAN TRS ISNMTS QEFVEKLTKR LKRHPEETGG FQEAPLAYDA IWALALALNK TSGGGGRSGV RLEDFNYNNQ TITDQIYRAM NSSS FEGVS GHVVFDASGS RMAWTLIEQL QGGSYKKIGY YDSTKDDLSW SKTDKWIGGS PPADQTLVIK TFRFLSQKLF ISVSV LSSL GIVLAVVCLS FNIYNSHVRY IQNSQPNLNN LTAVGCSLAL AAVFPLGLDG YHIGRNQFPF VCQARLWLLG LGFSLG YGS MFTKIWWVHT VFTKKEEKKE WRKTLEPWKL YATVGLLVGM DVLTLAIWQI VDPLHRTIET FAKEEPKEDI DVSILPQ LE HCSSRKMNTW LGIFYGYKGL LLLLGIFLAY ETKSVSTEKI NDHRAVGMAI YNVAVLCLIT APVTMILSSQ QDAAFAFA S LAIVFSSYIT LVVLFVPKMR RLITRGEWQS EAQDTMKTGS STNNNEEEKS RLLEKENREL EKIIAEKEER VSELRHQLQ SRDYKDDDDK UniProtKB: Gamma-aminobutyric acid type B receptor subunit 1 |
-Macromolecule #2: Gamma-aminobutyric acid type B receptor subunit 2
Macromolecule | Name: Gamma-aminobutyric acid type B receptor subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 93.278781 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASPRSSGQP GPPPPPPPPP ARLLLLLLLP LLLPLAPGAW GWARGAPRPP PSSPPLSIMG LMPLTKEVAK GSIGRGVLPA VELAIEQIR NESLLRPYFL DLRLYDTECD NAKGLKAFYD AIKYGPNHLM VFGGVCPSVT SIIAESLQGW NLVQLSFAAT T PVLADKKK ...String: MASPRSSGQP GPPPPPPPPP ARLLLLLLLP LLLPLAPGAW GWARGAPRPP PSSPPLSIMG LMPLTKEVAK GSIGRGVLPA VELAIEQIR NESLLRPYFL DLRLYDTECD NAKGLKAFYD AIKYGPNHLM VFGGVCPSVT SIIAESLQGW NLVQLSFAAT T PVLADKKK YPYFFRTVPS DNAVNPAILK LLKHYQWKRV GTLTQDVQRF SEVRNDLTGV LYGEDIEISD TESFSNDPCT SV KKLKGND VRIILGQFDQ NMAAKVFCCA YEENMYGSKY QWIIPGWYEP SWWEQVHTEA NSSRCLRKNL LAAMEGYIGV DFE PLSSKQ IKTISGKTPQ QYEREYNNKR SGVGPSKFHG YAYDGIWVIA KTLQRAMETL HASSRHQRIQ DFNYTDHTLG RIIL NAMNE TNFFGVTGQV VFRNGERMGT IKFTQFQDSR EVKVGEYNAV ADTLEIINDT IRFQGSEPPK DKTIILEQLR KISLP LYSI LSALTILGMI MASAFLFFNI KNRNQKLIKM SSPYMNNLII LGGMLSYASI FLFGLDGSFV SEKTFETLCT VRTWIL TVG YTTAFGAMFA KTWRVHAIFK NVKMKKKIIK DQKLLVIVGG MLLIDLCILI CWQAVDPLRR TVEKYSMEPD PAGRDIS IR PLLEHCENTH MTIWLGIVYA YKGLLMLFGC FLAWETRNVS IPALNDSKYI GMSVYNVGIM CIIGAAVSFL TRDQPNVQ F CIVALVIIFC STITLCLVFV PKLITLRTNP DAATQNRRFQ FTQNQKKEDS KTSTSVTSVN QASTSRLEGL QSENHRLRM KITELDKDLE EVTMQLQDTD YKDDDDK UniProtKB: Gamma-aminobutyric acid type B receptor subunit 2 |
-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: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-{[(9Z)-oct...
Macromolecule | Name: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-{[(9Z)-octadec-9-enoyl]oxy}propyl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate type: ligand / ID: 5 / Number of copies: 1 / Formula: U3G |
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Molecular weight | Theoretical: 766.039 Da |
Chemical component information | ChemComp-U3G: |
-Macromolecule #6: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 10 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #7: [(2R)-3-[(Z)-icos-11-enoyl]oxy-2-[(Z)-octadec-9-enoyl]oxypropyl] ...
Macromolecule | Name: [(2R)-3-[(Z)-icos-11-enoyl]oxy-2-[(Z)-octadec-9-enoyl]oxypropyl] 2-(trimethylazaniumyl)ethyl phosphate type: ligand / ID: 7 / Number of copies: 1 / Formula: U3D |
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Molecular weight | Theoretical: 814.167 Da |
Chemical component information | ChemComp-U3D: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Solutions were made fresh from concentrated and filtered to avoid microbial contamination. | |||||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging. | |||||||||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Max: 100.0 K |
Specialist optics | Energy filter - Slit width: 20 eV |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 3435 / Average exposure time: 12.0 sec. / Average electron dose: 85.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 130000 |
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
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||
Output model | PDB-6wiv: |