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- PDB-6ksp: Rat GluD1 receptor(splayed conformation) in complex with 7-CKA an... -

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Basic information

Entry
Database: PDB / ID: 6ksp
TitleRat GluD1 receptor(splayed conformation) in complex with 7-CKA and Calcium ions
ComponentsGlutamate receptor ionotropic, delta-1
KeywordsMEMBRANE PROTEIN / complex
Function / homology
Function and homology information


GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels ...GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / GABA-ergic synapse / phospholipase C-activating G protein-coupled receptor signaling pathway / dendritic spine / postsynaptic membrane / glutamatergic synapse / metal ion binding / identical protein binding / 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-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsBurada, A.P. / Kumar, J.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/5010023 India
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structures of the ionotropic glutamate receptor GluD1 reveal a non-swapped architecture.
Authors: Ananth Prasad Burada / Rajesh Vinnakota / Janesh Kumar /
Abstract: Ionotropic orphan delta (GluD) receptors are not gated by glutamate or any other endogenous ligand but are grouped with ionotropic glutamate receptors (iGluRs) based on sequence similarity. GluD1 ...Ionotropic orphan delta (GluD) receptors are not gated by glutamate or any other endogenous ligand but are grouped with ionotropic glutamate receptors (iGluRs) based on sequence similarity. GluD1 receptors play critical roles in synaptogenesis and synapse maintenance and have been implicated in neuronal disorders, including schizophrenia, cognitive deficits, and cerebral ataxia. Here we report cryo-EM structures of the rat GluD1 receptor complexed with calcium and the ligand 7-chlorokynurenic acid (7-CKA), elucidating molecular architecture and principles of receptor assembly. The structures reveal a non-swapped architecture at the interface of the extracellular amino-terminal domain (ATD) and the ligand-binding domain (LBD). This finding is in contrast with structures of other families of iGluRs, where the dimer partners between the ATD and LBD layers are swapped. Our results demonstrate that principles of architecture and symmetry are not conserved between delta receptors and other iGluRs and provide a molecular blueprint for understanding the functions of the 'orphan' class of iGluRs.
History
DepositionAug 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, delta-1
B: Glutamate receptor ionotropic, delta-1
C: Glutamate receptor ionotropic, delta-1
D: Glutamate receptor ionotropic, delta-1


Theoretical massNumber of molelcules
Total (without water)382,8724
Polymers382,8724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19230 Å2
ΔGint-101 kcal/mol
Surface area154860 Å2

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Components

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


Mass: 95718.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grid1 / Plasmid: pEGBacMam / Cell line (production host): HEK293SGnTI- / Production host: Homo sapiens (human) / References: UniProt: Q62640
Compound detailsThe distance between Residue A LYS 527 and Residue A ILE 532 is 20.50 Angstrom. The distance ...The distance between Residue A LYS 527 and Residue A ILE 532 is 20.50 Angstrom. The distance between Residue B LYS 527 and Residue B ILE 532 is 22.35 Angstrom. The distance between Residue C LYS 527 and Residue C ILE 532 is 20.85 Angstrom.
Has protein modificationY
Sequence detailsThrombin recognition site

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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: GluD1 / 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
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
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

EM software
IDNameVersionCategoryDetails
1cryoSPARCv2.9.0particle selectiontemplate picker
2EPUimage acquisitionFEI EPU
4Gctfv1.06CTF correctionGctf
7UCSF Chimera1.12model fitting
9cryoSPARCv2.9.0initial Euler assignment
10cryoSPARCv2.9.0final Euler assignmentlocal refinement
11cryoSPARCv2.9.0classification
12cryoSPARCv2.9.03D reconstruction
19PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2000
Details: Particles were picked manually, which were used as reference for autopicking.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14939 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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