+Open data
-Basic information
Entry | Database: PDB / ID: 8trd | ||||||||||||
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Title | mGluR3 class 1 in the presence of the antagonist LY 341495 | ||||||||||||
Components | Metabotropic glutamate receptor 3 | ||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / synaptic protein | ||||||||||||
Function / homology | Function and homology information Class C/3 (Metabotropic glutamate/pheromone receptors) / group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / G alpha (i) signalling events / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / sensory perception of pain / modulation of chemical synaptic transmission ...Class C/3 (Metabotropic glutamate/pheromone receptors) / group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / G alpha (i) signalling events / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / sensory perception of pain / modulation of chemical synaptic transmission / presynaptic membrane / gene expression / scaffold protein binding / postsynapse / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / glutamatergic synapse / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Strauss, A. / Levitz, J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To be published Title: Structural basis of allosteric modulation of metabotropic glutamate receptor activation and desensitization Authors: Strauss, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8trd.cif.gz | 289.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8trd.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 8trd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8trd_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8trd_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8trd_validation.xml.gz | 58.7 KB | Display | |
Data in CIF | 8trd_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/8trd ftp://data.pdbj.org/pub/pdb/validation_reports/tr/8trd | HTTPS FTP |
-Related structure data
Related structure data | 41578MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 103161.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grm3 / Production host: Homo sapiens (human) / References: UniProt: P31422 #2: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Metabotropic Glutamate Receptor 3 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.26 MDa / Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 58 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84964 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.26 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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