+Open data
-Basic information
Entry | Database: PDB / ID: 6jfz | |||||||||
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Title | GluK3 receptor complex with UBP310 | |||||||||
Components | Glutamate receptor ionotropic, kainate 3 | |||||||||
Keywords | MEMBRANE PROTEIN / Glutamate receptor / Kainate / UBP310 | |||||||||
Function / homology | Function and homology information Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity ...Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / synaptic transmission, glutamatergic / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / axon / glutamatergic synapse / dendrite / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | Kumari, J. / Kumar, J. | |||||||||
Funding support | India, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery. Authors: Jyoti Kumari / Rajesh Vinnakota / Janesh Kumar / Abstract: GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better ...GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. While the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a resting state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using structures as a guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. The mutational analysis also identified putative N-glycan interacting residues. Our results provide a molecular framework for understanding gating properties unique to GluK3 and exploring the role of N-linked glycosylation in their modulation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jfz.cif.gz | 493.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jfz.ent.gz | 421.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/6jfz ftp://data.pdbj.org/pub/pdb/validation_reports/jf/6jfz | HTTPS FTP |
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-Related structure data
Related structure data | 9822MC 9821C 6jfyC 6jmvC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 91305.812 Da / Num. of mol.: 4 / Mutation: C86T, C305T, C547V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, Glur7 / Plasmid: pEG BacMAM / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P42264 Sequence details | The sequence conflicts A259P/S310P/P324A are based on AAC80577 (PubMed:1371217) according to ...The sequence conflicts A259P/S310P/P324A are based on AAC80577 (PubMed:1371217) according to database P42264 (GRIK3_RAT). | |
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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: GluK3 complex with agonist SYM / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.4 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Rattus norvegicus (Norway rat) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 / Plasmid: pEG BacMAM | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified and detergent solubilized GluK3 receptors | |||||||||||||||||||||||||
Vitrification | 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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 16.73 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 719 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27194 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |