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Yorodumi- EMDB-31537: Thermostabilised full length human mGluR5-5M with orthosteric ant... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31537 | ||||||||||||||||||
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Title | Thermostabilised full length human mGluR5-5M with orthosteric antagonist, LY341495 | ||||||||||||||||||
Map data | Post processed map from Relion, with a B-factor sharpening of -82 | ||||||||||||||||||
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 / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / astrocyte projection ...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 / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) / : / glutamate receptor activity / Neurexins and neuroligins / protein tyrosine kinase activator activity / : / regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / dendritic shaft / learning / locomotory behavior / G protein-coupled receptor activity / postsynaptic density membrane / synapse organization / Schaffer collateral - CA1 synapse / cognition / 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 | Vinothkumar KR / Cannone G / Lebon G | ||||||||||||||||||
Funding support | India, United Kingdom, France, 5 items
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Citation | Journal: Cell Rep / Year: 2021 Title: Agonists and allosteric modulators promote signaling from different metabotropic glutamate receptor 5 conformations. Authors: Chady Nasrallah / Giuseppe Cannone / Julie Briot / Karine Rottier / Alice E Berizzi / Chia-Ying Huang / Robert B Quast / Francois Hoh / Jean-Louis Banères / Fanny Malhaire / Ludovic Berto / ...Authors: Chady Nasrallah / Giuseppe Cannone / Julie Briot / Karine Rottier / Alice E Berizzi / Chia-Ying Huang / Robert B Quast / Francois Hoh / Jean-Louis Banères / Fanny Malhaire / Ludovic Berto / Anaëlle Dumazer / Joan Font-Ingles / Xavier Gómez-Santacana / Juanlo Catena / Julie Kniazeff / Cyril Goudet / Amadeu Llebaria / Jean-Philippe Pin / Kutti R Vinothkumar / Guillaume Lebon / Abstract: Metabotropic glutamate receptors (mGluRs) are dimeric G-protein-coupled receptors activated by the main excitatory neurotransmitter, L-glutamate. mGluR activation by agonists binding in the venus ...Metabotropic glutamate receptors (mGluRs) are dimeric G-protein-coupled receptors activated by the main excitatory neurotransmitter, L-glutamate. mGluR activation by agonists binding in the venus flytrap domain is regulated by positive (PAM) or negative (NAM) allosteric modulators binding to the 7-transmembrane domain (7TM). We report the cryo-electron microscopy structures of fully inactive and intermediate-active conformations of mGlu receptor bound to an antagonist and a NAM or an agonist and a PAM, respectively, as well as the crystal structure of the 7TM bound to a photoswitchable NAM. The agonist induces a large movement between the subunits, bringing the 7TMs together and stabilizing a 7TM conformation structurally similar to the inactive state. Using functional approaches, we demonstrate that the PAM stabilizes a 7TM active conformation independent of the conformational changes induced by agonists, representing an alternative mode of mGlu activation. These findings provide a structural basis for different mGluR activation modes. | ||||||||||||||||||
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_31537.map.gz | 93.1 MB | EMDB map data format | |
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Header (meta data) | emd-31537-v30.xml emd-31537.xml | 27.7 KB 27.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31537_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_31537.png | 44.1 KB | ||
Others | emd_31537_additional_1.map.gz emd_31537_additional_2.map.gz emd_31537_half_map_1.map.gz emd_31537_half_map_2.map.gz | 92 MB 95 MB 79.3 MB 79.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31537 | HTTPS FTP |
-Validation report
Summary document | emd_31537_validation.pdf.gz | 766.7 KB | Display | EMDB validaton report |
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Full document | emd_31537_full_validation.pdf.gz | 766.3 KB | Display | |
Data in XML | emd_31537_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_31537_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31537 | HTTPS FTP |
-Related structure data
Related structure data | 7fd9MC 7fd8C 7p2lC 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_31537.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Post processed map from Relion, with a B-factor sharpening of -82 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.89 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Postprocessed map sharpened with a B factor of...
File | emd_31537_additional_1.map | ||||||||||||
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Annotation | Postprocessed map sharpened with a B factor of -20, used in model building | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Postprocessed map sharpened with a B factor of...
File | emd_31537_additional_2.map | ||||||||||||
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Annotation | Postprocessed map sharpened with a B factor of -164, used in model building | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: One of the half map from refinement
File | emd_31537_half_map_1.map | ||||||||||||
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Annotation | One of the half map from refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: One of the half map from refinement
File | emd_31537_half_map_2.map | ||||||||||||
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Annotation | One of the half map from refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human FL mGluR5-5M with orthosteric antagonist LY341495 and NAM MPEP
Entire | Name: Human FL mGluR5-5M with orthosteric antagonist LY341495 and NAM MPEP |
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Components |
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-Supramolecule #1: Human FL mGluR5-5M with orthosteric antagonist LY341495 and NAM MPEP
Supramolecule | Name: Human FL mGluR5-5M with orthosteric antagonist LY341495 and NAM MPEP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI- |
Molecular weight | Theoretical: 194 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: 96.953977 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DYKDDDDKHH HHHHHHHHLE VLFQGPQSSE RRVVAHMPGD IIIGALFSVH HQPTVDKVHE RKCGAVREQY GIQRVEAMLH TLERINSDP TLLPNITLGC EIRDSCWHSA VALEQSIEFI RDSLISSEEE EGLVRCVDGS SSSFRSKKPI VGVIGPGSSS V AIQVQNLL ...String: DYKDDDDKHH HHHHHHHHLE VLFQGPQSSE 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 YLKLRPETNL RNPWFQEFWQ HRFQCRLEGF PQENSKYNKT CNSSLTLKTH HVQD SKMGF VINAIYSMAY GLHNMQMSLC PGYAGLCDAM KPIDGRKLLE SLMKTAFTGV 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 TNLGVVAPLG YNGLLILACT FYAFKTRNVP ANFNEAKYIA FAMYTTCIIW LAFVPIYFG SNYKAITMCF SVSLSATVLL GCMFVPKVYI ILAKPERNVR SAFTTSTVVR MHVGDGKSSS AA |
-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: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #3: 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine
Macromolecule | Name: 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine type: ligand / ID: 3 / Number of copies: 2 / Formula: Z99 |
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Molecular weight | Theoretical: 353.369 Da |
Chemical component information | ChemComp-Z99: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force was 10, 3.5 seconds blotting time. | |||||||||
Details | mGluR5 with orthosteric antagonist LY341495 and NAM (MPEP) purified in DDM/CHS |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV Details: Imaging was done in EFTEM mode. Images were collected using beam shift in a series of 3x3 holes before stage shift. Active beam tilt compensation was turned on during the acquisition. |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 16668 / Average exposure time: 5.2 sec. / Average electron dose: 49.9 e/Å2 Details: Dose rate was 7.6 e/p/s. Total number of frames is 32 and each frame has a dose of 1.56 e/A2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 44500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 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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Details | Refinement was performed with jelly body restraints | ||||||
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 147.5 | ||||||
Output model | PDB-7fd9: |