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- PDB-6l6f: GluK3 receptor complex with UBP301 -

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Basic information

Entry
Database: PDB / ID: 6l6f
TitleGluK3 receptor complex with UBP301
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / dendrite / glutamatergic synapse / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.6 Å
AuthorsKumar, J. / Kumari, J. / Burada, A.P.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/501023 India
CitationJournal: Int J Biol Macromol / Year: 2020
Title: Structural dynamics of the GluK3-kainate receptor neurotransmitter binding domains revealed by cryo-EM.
Authors: Jyoti Kumari / Ameya D Bendre / Sumedha Bhosale / Rajesh Vinnakota / Ananth P Burada / Giancarlo Tria / Raimond B G Ravelli / Peter J Peters / Manali Joshi / Janesh Kumar /
Abstract: Kainate receptors belong to the ionotropic glutamate receptor family and play critical roles in the regulation of synaptic networks. The kainate receptor subunit GluK3 has unique functional ...Kainate receptors belong to the ionotropic glutamate receptor family and play critical roles in the regulation of synaptic networks. The kainate receptor subunit GluK3 has unique functional properties and contributes to presynaptic facilitation at the hippocampal mossy fiber synapses along with roles at the post-synapses. To gain structural insights into the unique functional properties and dynamics of GluK3 receptor, we imaged them via electron microscopy in the apo-state and in complex with either agonist kainate or antagonist UBP301. Our analysis of all the GluK3 full-length structures not only provides insights into the receptor transitions between desensitized and closed states but also reveals a "non-classical" conformation of neurotransmitter binding domain in the closed-state distinct from that observed in AMPA and other kainate receptor structures. We show by molecular dynamics simulations that Asp759 influences the stability of the LBD dimers and hence could be responsible for the observed conformational variability and dynamics of the GluK3 via electron microscopy. Lower dimer stability could explain faster desensitization and low agonist sensitivity of GluK3. In overview, our work helps to associate biochemistry and physiology of GluK3 receptors with their structural biology and offers structural insights into the unique functional properties of these atypical receptors.
History
DepositionOct 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 3
B: Glutamate receptor ionotropic, kainate 3
C: Glutamate receptor ionotropic, kainate 3
D: Glutamate receptor ionotropic, kainate 3


Theoretical massNumber of molelcules
Total (without water)375,9404
Polymers375,9404
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16840 Å2
ΔGint-136 kcal/mol
Surface area134700 Å2

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Components

#1: Protein
Glutamate receptor ionotropic, kainate 3 / Glutamate receptor / ionotropic / kainate 3 / isoform CRA_b


Mass: 93984.922 Da / Num. of mol.: 4 / Mutation: T117C, T336C, V578C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, rCG_30794 / Plasmid: pEGBacMam / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: G3V9I2, UniProt: P42264*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GluK3 complex with agonist Kainate / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: YES
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 GnTi- / Plasmid: pEGBacMam
Buffer solutionpH: 8 / Details: 20 mM Tris pH 8.0, 150 mM NaCl
Buffer componentConc.: 1.7 1.7 / Name: Sodium Chloride / Formula: NaCl
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationCryogen name: ETHANE / Details: Multiple application, blotted for 3 seconds

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 16.73 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2845

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2cryoSPARCv1image acquisition
3RELION2.1image acquisition
4Gctfv1.06image acquisition
5UCSF Chimera1.14image acquisition
6PHENIX1.16-3549image acquisition
8Gctfv1.06CTF correction
17cryoSPARCv13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 46106
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 10.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27997 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 6JFY

6jfy


Accession code: 6JFY / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00623351
ELECTRON MICROSCOPYf_angle_d1.21131611
ELECTRON MICROSCOPYf_dihedral_angle_d15.77413931
ELECTRON MICROSCOPYf_chiral_restr0.0633564
ELECTRON MICROSCOPYf_plane_restr0.013991

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