+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0346 | |||||||||
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Title | Metabotropic Glutamate Receptor 5 Apo Form | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / positive regulation of long-term neuronal synaptic plasticity / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / desensitization of G protein-coupled receptor signaling pathway / astrocyte projection / G protein-coupled glutamate receptor signaling pathway ...A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / positive regulation of long-term neuronal synaptic plasticity / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / desensitization of G protein-coupled receptor signaling pathway / astrocyte projection / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / glutamate receptor activity / Neurexins and neuroligins / protein tyrosine kinase activator activity / regulation of synaptic transmission, glutamatergic / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / learning / dendritic shaft / cognition / locomotory behavior / G protein-coupled receptor activity / postsynaptic density membrane / synapse organization / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / G alpha (q) signalling events / chemical synaptic transmission / positive regulation of MAPK cascade / dendritic spine / learning or memory / glutamatergic synapse / dendrite / regulation of DNA-templated transcription / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Koehl A / Hu H / Feng D / Sun B / Weis WI / Skiniotis GS / Mathiesen JM / Kobilka BK | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2019 Title: Structural insights into the activation of metabotropic glutamate receptors. Authors: Antoine Koehl / Hongli Hu / Dan Feng / Bingfa Sun / Yan Zhang / Michael J Robertson / Matthew Chu / Tong Sun Kobilka / Toon Laeremans / Jan Steyaert / Jeffrey Tarrasch / Somnath Dutta / ...Authors: Antoine Koehl / Hongli Hu / Dan Feng / Bingfa Sun / Yan Zhang / Michael J Robertson / Matthew Chu / Tong Sun Kobilka / Toon Laeremans / Jan Steyaert / Jeffrey Tarrasch / Somnath Dutta / Rasmus Fonseca / William I Weis / Jesper M Mathiesen / Georgios Skiniotis / Brian K Kobilka / Abstract: Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich ...Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectroscopic studies show that signalling is a dynamic process, in which large-scale conformational changes underlie the transmission of signals from the extracellular Venus flytraps to the G protein-coupling domains-the 7-transmembrane domains-in the membrane. Here, using a combination of X-ray crystallography, cryo-electron microscopy and signalling studies, we present a structural framework for the activation mechanism of metabotropic glutamate receptor subtype 5. Our results show that agonist binding at the Venus flytraps leads to a compaction of the intersubunit dimer interface, thereby bringing the cysteine-rich domains into close proximity. Interactions between the cysteine-rich domains and the second extracellular loops of the receptor enable the rigid-body repositioning of the 7-transmembrane domains, which come into contact with each other to initiate signalling. | |||||||||
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_0346.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-0346-v30.xml emd-0346.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
Images | emd_0346.png | 146.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0346 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0346 | HTTPS FTP |
-Validation report
Summary document | emd_0346_validation.pdf.gz | 454.9 KB | Display | EMDB validaton report |
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Full document | emd_0346_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | emd_0346_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_0346_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0346 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0346 | HTTPS FTP |
-Related structure data
Related structure data | 6n52MC 0345C 0347C 6n4xC 6n4yC 6n50C 6n51C 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_0346.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Metabotropic Glutamate Receptor 5 in Nanodiscs
Entire | Name: Metabotropic Glutamate Receptor 5 in Nanodiscs |
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Components |
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-Supramolecule #1: Metabotropic Glutamate Receptor 5 in Nanodiscs
Supramolecule | Name: Metabotropic Glutamate Receptor 5 in Nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Metabotropic Glutamate Receptor 5 in Nanodiscs |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Metabotropic glutamate receptor 5
Macromolecule | Name: Metabotropic glutamate receptor 5 / 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: 97.677945 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDAAAQSSE RRVVAHMPGD IIIGALFSVH HQPTVDKVHE RKCGAVREQY GIQRVEAMLH TLERINSDP TLLPNITLGC EIRDSCWHSA VALEQSIEFI RDSLISSEEE EGLVRCVDGS SSSFRSKKPI VGVIGPGSSS V AIQVQNLL ...String: MKTIIALSYI FCLVFADYKD DDDAAAQSSE RRVVAHMPGD IIIGALFSVH HQPTVDKVHE RKCGAVREQY GIQRVEAMLH TLERINSDP TLLPNITLGC EIRDSCWHSA VALEQSIEFI RDSLISSEEE EGLVRCVDGS SSSFRSKKPI VGVIGPGSSS V AIQVQNLL QLFNIPQIAY SATSMDLSDK TLFKYFMRVV PSDAQQARAM VDIVKRYNWT YVSAVHTEGN YGESGMEAFK DM SAKEGIC IAHSYKIYSN AGEQSFDKLL KKLTSHLPKA RVVACFCEGM TVRGLLMAMR RLGLAGEFLL LGSDGWADRY DVT DGYQRE AVGGITIKLQ SPDVKWFDDY YLKLRPETNH RNPWFQEFWQ HRFQCRLEGF PQENSKYNKT CNSSLTLKTH HVQD SKMGF VINAIYSMAY GLHNMQMSLC PGYAGLCDAM KPIDGRKLLE SLMKTNFTGV SGDTILFDEN GDSPGRYEIM NFKEM GKDY FDYINVGSWD NGELKMDDDE VWSKKSNIIR SVCSEPCEKG QIKVIRKGEV SCCWTCTPCK ENEYVFDEYT CKACQL GSW PTDDLTGCDL IPVQYLRWGD PEPIAAVVFA CLGLLATLFV TVVFIIYRDT PVVKSSSREL CYIILAGICL GYLCTFC LI AKPKQIYCYL QRIGIGLSPA MSYSALVTKT NRIARILAGS KKKICTKKPR FMSACAQLVI AFILICIQLG IIVALFIM E PPDIMHDYPS IREVYLICNT TNLGVVTPLG YNGLLILSCT FYAFKTRNVP ANFNEAKYIA FTMYTTCIIW LAFVPIYFG SNYKIITMCF SVSLSATVAL GCMFVPKVYI ILAKPERNVR SAFTTSTVVR MHVGDGKSSS AASRSSSLVN L |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: 100mM NaCl, 20 mM HEPES pH 7.5, 5uM FFMTEB added as a negative allosteric modulator. | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV Details: Addition 0.0005% Amphipol A8-35was added to sample prior to apply to grid; 3.5ul sample was applied; blot for 1s before plunging. | |||||||||
Details | This sample was mono disperse as assayed by gel filtration. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 47169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Ab initio model was generated from VIPER. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 123096 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |