+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0347 | |||||||||
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Title | Apo form metabotropic glutamate receptor 5 with Nanobody 43 | |||||||||
Map data | Apo form metabotropic glutamate receptor 5 with Nanobody 43, primary map | |||||||||
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) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.9 Å | |||||||||
Authors | Koehl A / Hu H / Feng D / Zhang Y / Sun B / Kobilka TS / Pardon E / Steyaert J / Mathiesen JM / Skiniotis G / Kobilka BK | |||||||||
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_0347.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-0347-v30.xml emd-0347.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_0347.png | 30.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0347 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0347 | HTTPS FTP |
-Validation report
Summary document | emd_0347_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_0347_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_0347_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0347 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0347 | HTTPS FTP |
-Related structure data
Related structure data | 0345C 0346C 6n4xC 6n4yC 6n50C 6n51C 6n52C C: citing same article (ref.) |
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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_0347.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Apo form metabotropic glutamate receptor 5 with Nanobody 43, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.58 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 - Nb43 Complex
Entire | Name: Metabotropic Glutamate Receptor 5 - Nb43 Complex |
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Components |
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-Supramolecule #1: Metabotropic Glutamate Receptor 5 - Nb43 Complex
Supramolecule | Name: Metabotropic Glutamate Receptor 5 - Nb43 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Complex between metabotropic glutamate receptor 5 and Nb43 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: SF9 |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: Metabotropic Glutamate Receptor 5
Macromolecule | Name: Metabotropic Glutamate Receptor 5 / type: protein_or_peptide / ID: 1 Details: Polypeptide encoding metabotropic glutamate receptor 5 Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: QSSERRVVAH MPGDIIIGAL FSVHHQPTVD KVHERKCGAV REQYGIQRV EAMLHTLERI NSDPTLLPNI TLGCEIRDSC WHSAVALEQS IEFIRDSLIS S EEEEGLVR CVDGSSSSFR SKKPIVGVIG PGSSSVAIQV QNLLQLFNIP QIAYSATSMD LS DKTLFKY ...String: QSSERRVVAH MPGDIIIGAL FSVHHQPTVD KVHERKCGAV REQYGIQRV EAMLHTLERI NSDPTLLPNI TLGCEIRDSC WHSAVALEQS IEFIRDSLIS S EEEEGLVR CVDGSSSSFR SKKPIVGVIG PGSSSVAIQV QNLLQLFNIP QIAYSATSMD LS DKTLFKY FMRVVPSDAQ QARAMVDIVK RYNWTYVSAV HTEGNYGESG MEAFKDMSAK EGI CIAHSY KIYSNAGEQS FDKLLKKLTS HLPKARVVAC FCEGMTVRGL LMAMRRLGLA GEFL LLGSD GWADRYDVTD GYQREAVGGI TIKLQSPDVK WFDDYYLKLR PETNHRNPWF QEFWQ HRFQ CRLEGFPQEN SKYNKTCNSS LTLKTHHVQD SKMGFVINAI YSMAYGLHNM QMSLCP GYA GLCDAMKPID GRKLLESLMK TNFTGVSGDT ILFDENGDSP GRYEIMNFKE MGKDYFD YI NVGSWDNGEL KMDDDEVWSK KSNIIRSVCS EPCEKGQIKV IRKGEVSCCW TCTPCKEN E YVFDEYTCKA CQLGSWPTDD LTGCDLIPVQ YLRWGDPEPI AAVVFACLGL LATLFVTVV FIIYRDTPVV KSSSRELCYI ILAGICLGYL CTFCLIAKPK QIYCYLQRIG IGLSPAMSYS ALVTKTNRI ARILAGSKKK ICTKKPRFMS ACAQLVIAFI LICIQLGIIV ALFIMEPPDI M HDYPSIRE VYLICNTTNL GVVTPLGYNG LLILSCTFYA FKTRNVPANF NEAKYIAFTM YT TCIIWLA FVPIYFGSNY KIITMCFSVS LSATVALGCM FVPKVYIILA KPERNVRSAF TTS TVVRMH VGDGKSSSAA SRSSSLVNL |
-Macromolecule #2: Nanobody 43
Macromolecule | Name: Nanobody 43 / type: protein_or_peptide / ID: 2 / Details: Nanobody 43 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLVESGGG LVQAGGSLRL SCAASGRTFT SYAMGWFRQA PGKERESVAA ISSSGGSTHY ADSVKGRFTI SRDNSKNTVY LQMNSLKPED TAVYYCAAAM YGSRWPDWEY DYWGQGTQVT VSSAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE | |||||||||||||||
Details | Sample was mono disperse as assayed by gel filtration and SDS PAGE. |
-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: 58139 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: The apo structure was used as starting model. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 44831 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |