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- PDB-7ysj: GluK1-1a in nanodisc captured in SYM2081 bound desensitized state -

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Basic information

Entry
Database: PDB / ID: 7ysj
TitleGluK1-1a in nanodisc captured in SYM2081 bound desensitized state
ComponentsGlutamate receptor
KeywordsMEMBRANE PROTEIN / Kainate receptor / GluK1-1a splice variant / nanodisc / SYM2081 bound / desensitized state
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: 5.2 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 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Refinement description / Category: citation / citation_author / em_3d_fitting_list
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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)498,1094
Polymers498,1094
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: 124527.125 Da / Num. of mol.: 4 / Mutation: C552Y, C557V
Source method: isolated from a genetically manipulated source
Details: L838-S843 correspond to Thrombin recognition site, A844-A847 correspond to Ala linker, V848-S1090 correspond to enhanced green fluorescent protein (EGFP), H1091-H1098 correspond to Octa-His affinity tag.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, rCG_58820 / Variant: 1 / Cell line (production host): HEK 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: Complex of GluK1-1a in lipid nanodisc with SYM2081 / Type: COMPLEX
Details: EGFP is covalently conjugated to the C-terminus of GluK1-1a. MSP1E3D1 soybean polar lipid nanodisc used.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.60 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pEGBacMam
Buffer solutionpH: 8
SpecimenConc.: 0.87 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: 12 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24531 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13C32

3c32

13C321PDBexperimental model
25KUF

5kuf

15KUF2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322004
ELECTRON MICROSCOPYf_angle_d0.79529772
ELECTRON MICROSCOPYf_dihedral_angle_d5.5122960
ELECTRON MICROSCOPYf_chiral_restr0.0473328
ELECTRON MICROSCOPYf_plane_restr0.0063780

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