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- PDB-8gpr: GluK1-1a receptor captured in the desensitized state -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8gpr
TitleGluK1-1a receptor captured in the desensitized state
ComponentsGlutamate receptor
KeywordsMEMBRANE PROTEIN / Kainate receptor
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / signaling receptor activity / postsynaptic membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsDhingra, S. / Kumar, J.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2020/003971 India
CitationJournal: Elife / Year: 2023
Title: Functional Implications of the Exon 9 Splice Insert in GluK1 Kainate Receptors
Authors: Dhingra, S. / Chopade, P.M. / Vinnakota, R. / Kumar, J.
History
DepositionAug 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor
B: Glutamate receptor
C: Glutamate receptor
D: Glutamate receptor


Theoretical massNumber of molelcules
Total (without water)382,4274
Polymers382,4274
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Fluorescence assisted size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glutamate receptor /


Mass: 95606.672 Da / Num. of mol.: 4 / Mutation: C552Y, C557V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1 / Plasmid: pEGBacMam / Cell line (production host): HEK293 GnTI negative / Production host: Homo sapiens (human) / References: UniProt: A0A0G2K830

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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: GluK1-1a receptor in complex with SYM2081 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.381 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pEGBacMam
Buffer solutionpH: 8
SpecimenConc.: 0.57 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 R0.6/1
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 60 sec. / Electron dose: 19.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARCv.3.2.0particle selection
12cryoSPARCv.3.2.03D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 13750
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5372 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00424383
ELECTRON MICROSCOPYf_angle_d0.89133033
ELECTRON MICROSCOPYf_dihedral_angle_d5.4593275
ELECTRON MICROSCOPYf_chiral_restr0.0473728
ELECTRON MICROSCOPYf_plane_restr0.0064167

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