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Yorodumi- PDB-8gc2: Domoate-bound GluK2 kainate receptor in partially-open conformation 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gc2 | ||||||
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Title | Domoate-bound GluK2 kainate receptor in partially-open conformation 1 | ||||||
Components | Glutamate receptor ionotropic, kainate 2 | ||||||
Keywords | MEMBRANE PROTEIN / ion channel / glutamate kainate receptor 2 / homotetramer / partial agonist / gating mechanism | ||||||
Function / homology | Function and homology information mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / regulation of membrane potential / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / synapse / ubiquitin protein ligase binding / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Bogdanovic, N. / Tajima, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structural basis for kainate receptor activation by a partial agonist Authors: Bogdanovic, N. / Tajima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gc2.cif.gz | 549.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gc2.ent.gz | 443.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gc2_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8gc2_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8gc2_validation.xml.gz | 97 KB | Display | |
Data in CIF | 8gc2_validation.cif.gz | 143.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/8gc2 ftp://data.pdbj.org/pub/pdb/validation_reports/gc/8gc2 | HTTPS FTP |
-Related structure data
Related structure data | 29926MC 8gc3C 8gc4C 8gc5C 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
-Protein / Non-polymers , 2 types, 7 molecules ABCD
#1: Protein | Mass: 98883.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P42260 #7: Chemical | |
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-Sugars , 5 types, 16 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Details
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: Homotetrameric GluK2 bound with domoate state 1 / Type: COMPLEX Details: Tetramer isolated and dyalised extensively. The domoate was applied prior to grid freezing. Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 / Details: 50 mM Tris/HCl 150 mM NaCl 1mM DDM pH 8.0 |
Buffer component | Conc.: 150 mmol / Name: sodium chloride / Formula: NaCl |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was isolated from SEC and concentrated. Monodispersity of the final sample determined by the analytical HPLC, S200i column. |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12486 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2481151 Details: Initially picked particles that are later classified in several rounds of 2D and 3D classifications. The number of final classes for this dataset is 4 of which this state represents "class ...Details: Initially picked particles that are later classified in several rounds of 2D and 3D classifications. The number of final classes for this dataset is 4 of which this state represents "class 1" and contains 39636 as the final number of particles. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39636 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 30 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: 0.85 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 209.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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