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- PDB-6lu9: Rat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA a... -

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Basic information

Entry
Database: PDB / ID: 6lu9
TitleRat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA and Calcium
ComponentsGlutamate receptor ionotropic, delta-2
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


cerebellar granule cell differentiation / excitatory synapse assembly / positive regulation of long-term synaptic depression / synaptic signaling via neuropeptide / regulation of postsynaptic density assembly / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / parallel fiber to Purkinje cell synapse / AMPA glutamate receptor activity ...cerebellar granule cell differentiation / excitatory synapse assembly / positive regulation of long-term synaptic depression / synaptic signaling via neuropeptide / regulation of postsynaptic density assembly / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / parallel fiber to Purkinje cell synapse / AMPA glutamate receptor activity / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / regulation of presynapse assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / prepulse inhibition / regulation of neuron apoptotic process / somatodendritic compartment / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / modulation of chemical synaptic transmission / postsynaptic density membrane / intracellular protein localization / scaffold protein binding / dendritic spine / postsynaptic membrane / synapse / glutamatergic synapse / identical protein binding / membrane / 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 ionotropic, delta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsKumar, J. / Burada, A.P.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/5010023 India
CitationJournal: J Struct Biol / Year: 2020
Title: The architecture of GluD2 ionotropic delta glutamate receptor elucidated by cryo-EM.
Authors: Ananth Prasad Burada / Rajesh Vinnakota / Janesh Kumar /
Abstract: GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple ...GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple neuronal disorders like schizophrenia, autism spectrum disorder, cerebellar ataxia, intellectual disability, paraplegia, retinal dystrophy, etc. Despite the importance of these receptors in CNS, insights into full-length GluD2 receptor structure is missing till-date. Here we report cryo-electron microscopy structure of the rat GluD2 receptor in the presence of calcium ions and the ligand 7-chlorokynurenic acid, elucidating its 3D architecture. The structure reveals a non-swapped architecture at the extracellular amino-terminal (ATD), and ligand-binding domain (LBD) interface similar to that observed in GluD1; however, the organization and arrangement of the ATD and LBD domains in GluD2 are unique. While our results demonstrate that non-swapped architecture is conserved in the delta receptor family, they also highlight the differences that exist between the two member receptors; GluD1 and GluD2.
History
DepositionJan 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 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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Assembly

Deposited unit
A: Glutamate receptor ionotropic, delta-2
B: Glutamate receptor ionotropic, delta-2
C: Glutamate receptor ionotropic, delta-2
D: Glutamate receptor ionotropic, delta-2


Theoretical massNumber of molelcules
Total (without water)394,7694
Polymers394,7694
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8360 Å2
ΔGint-22 kcal/mol
Surface area116920 Å2

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Components

#1: Protein
Glutamate receptor ionotropic, delta-2 / GluR delta-2 subunit


Mass: 98692.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grid2 / Plasmid: pEGBacMam / Production host: Homo sapiens (human) / References: UniProt: Q63226
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: GluD2 / Type: COMPLEX / Details: Recombinantly expressed protein / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.388 MDa / Experimental value: YES
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTI- / Plasmid: pEG Bac Mam
Buffer solutionpH: 8 / Details: 20mM Tris, 150mM NaCl, 0.75mM DDM, 0.025mM CHS
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6 sec. / Electron dose: 40.38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4120
Image scansMovie frames/image: 40 / Used frames/image: 0-40

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisitionFEI EPU
4Gctfv1.06CTF correctionGctf
7UCSF Chimera1.12model fitting
9PHENIX1.16model refinement
10cryoSPARCv2.13initial Euler assignment
11cryoSPARCv2.13final Euler assignmentlocal refinement
12cryoSPARCv2.13classification
13cryoSPARCv2.133D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 61332 / Details: Particles were picked manually
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7977 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02421416
ELECTRON MICROSCOPYf_angle_d2.53929020
ELECTRON MICROSCOPYf_dihedral_angle_d22.4447920
ELECTRON MICROSCOPYf_chiral_restr0.1443216
ELECTRON MICROSCOPYf_plane_restr0.0193792

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