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- PDB-7vm2: GluK3 D759G mutant receptor complex with UBP310 and spermine -

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Basic information

Entry
Database: PDB / ID: 7vm2
TitleGluK3 D759G mutant receptor complex with UBP310 and spermine
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / perikaryon / chemical synaptic transmission / postsynaptic membrane / axon / dendrite / glutamatergic synapse / 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, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsAssaiya, A. / Kumar, J.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2020/003971 India
CitationJournal: To Be Published
Title: GluK3 D759G mutant receptor in complex with UBP310 and Spermine
Authors: Assaiya, A. / Kumar, J.
History
DepositionOct 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 3
B: Glutamate receptor ionotropic, kainate 3
C: Glutamate receptor ionotropic, kainate 3
D: Glutamate receptor ionotropic, kainate 3


Theoretical massNumber of molelcules
Total (without water)364,9914
Polymers364,9914
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Fluorescence detection size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18850 Å2
ΔGint-160 kcal/mol
Surface area136100 Å2

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Components

#1: Protein
Glutamate receptor ionotropic, kainate 3 / GluK3 / Glutamate receptor 7 / GluR-7 / GluR7


Mass: 91247.781 Da / Num. of mol.: 4 / Mutation: C86T, C305T, C547V, D759G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, Glur7 / Variant: 1 / Cell line (production host): HEK293 GnTI negative / Production host: Homo sapiens (human) / References: UniProt: P42264
Has protein modificationY
Sequence detailsThe sequence conflicts A259P/S310P/P324A are based on AAC80577 (PubMed:1371217) according to ...The sequence conflicts A259P/S310P/P324A are based on AAC80577 (PubMed:1371217) according to database P42264 (GRIK3_RAT).

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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: GluK3 D759G mutant receptor complex with UBP310 and spermine
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.364 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pEGBacMam
Buffer solutionpH: 8
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in.
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 FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 43.72 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: cryoSPARC / Category: final Euler assignment
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56089 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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