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- PDB-7ks3: GluK2/K5 with L-Glu -

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Basic information

Entry
Database: PDB / ID: 7ks3
TitleGluK2/K5 with L-Glu
Components
  • Glutamate receptor ionotropic, kainate 2
  • Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
KeywordsSIGNALING PROTEIN / Kainate receptor / ionotropic glutamate receptor / membrane protein / ligand-gated ion channel
Function / homology
Function and homology information


regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / ubiquitin conjugating enzyme binding / regulation of JNK cascade / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / positive regulation of synaptic transmission / behavioral fear response / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / bioluminescence / hippocampal mossy fiber to CA3 synapse / SNARE binding / regulation of membrane potential / generation of precursor metabolites and energy / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to glucose stimulus / establishment of localization in cell / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / SH3 domain binding / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / neuron apoptotic process / scaffold protein binding / perikaryon / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / dendrite / synapse / ubiquitin protein ligase binding / glutamatergic synapse / endoplasmic reticulum / identical protein binding / membrane / plasma membrane
Similarity search - Function
Green fluorescent protein, GFP / 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 / : / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein ...Green fluorescent protein, GFP / 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 / : / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Green fluorescent protein / Glutamate receptor ionotropic, kainate 2 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsKhanra, N. / Brown, P.M.G.E. / Perozzo, A.M. / Bowie, D. / Meyerson, J.R.
CitationJournal: Elife / Year: 2021
Title: Architecture and structural dynamics of the heteromeric GluK2/K5 kainate receptor.
Authors: Nandish Khanra / Patricia Mge Brown / Amanda M Perozzo / Derek Bowie / Joel R Meyerson /
Abstract: Kainate receptors (KARs) are L-glutamate-gated ion channels that regulate synaptic transmission and modulate neuronal circuits. KARs have strict assembly rules and primarily function as heteromeric ...Kainate receptors (KARs) are L-glutamate-gated ion channels that regulate synaptic transmission and modulate neuronal circuits. KARs have strict assembly rules and primarily function as heteromeric receptors in the brain. A longstanding question is how KAR heteromer subunits organize and coordinate together to fulfill their signature physiological roles. Here we report structures of the GluK2/GluK5 heteromer in apo, antagonist-bound, and desensitized states. The receptor assembles with two copies of each subunit, ligand binding domains arranged as two heterodimers and GluK5 subunits proximal to the channel. Strikingly, during desensitization, GluK2, but not GluK5, subunits undergo major structural rearrangements to facilitate channel closure. We show how the large conformational differences between antagonist-bound and desensitized states are mediated by the linkers connecting the pore helices to the ligand binding domains. This work presents the first KAR heteromer structure, reveals how its subunits are organized, and resolves how the heteromer can accommodate functionally distinct closed channel structures.
History
DepositionNov 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 7, 2021Group: Derived calculations
Category: pdbx_struct_sheet_hbond / struct_conf ...pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
B: Glutamate receptor ionotropic, kainate 2
C: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
D: Glutamate receptor ionotropic, kainate 2


Theoretical massNumber of molelcules
Total (without water)459,3174
Polymers459,3174
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera / GluK5 / Glutamate receptor KA-2 / KA2


Mass: 123676.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Grik5, GFP / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q63273, UniProt: P42212
#2: Protein Glutamate receptor ionotropic, kainate 2 / GluK2 / Glutamate receptor 6 / GluR6


Mass: 105981.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P42260
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: GluK2/K5 with L-Glu / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTI-
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMsodium chlorideNaCl1
220 mMTris1
SpecimenConc.: 3.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 1 mM L-Glu
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 51.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: Leginon / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 573403
Details: Number of particles for ATD map: 241849 Number of particles for LBD-TMD map: 140028
Symmetry type: POINT

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