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- EMDB-0839: GluK3 receptor complex with UBP301 -

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Basic information

Entry
Database: EMDB / ID: EMD-0839
TitleGluK3 receptor complex with UBP301
Map datarefined and sharped map
Sample
  • Complex: GluK3 complex with agonist Kainate
    • Protein or peptide: Glutamate receptor ionotropic, kainate 3
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / monoatomic ion transmembrane transport / 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 / : / 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
Glutamate receptor / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.6 Å
AuthorsKumar J / Kumari J / Burada AP
Funding support India, 1 items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/501023 India
CitationJournal: Int J Biol Macromol / Year: 2020
Title: Structural dynamics of the GluK3-kainate receptor neurotransmitter binding domains revealed by cryo-EM.
Authors: Jyoti Kumari / Ameya D Bendre / Sumedha Bhosale / Rajesh Vinnakota / Ananth P Burada / Giancarlo Tria / Raimond B G Ravelli / Peter J Peters / Manali Joshi / Janesh Kumar /
Abstract: Kainate receptors belong to the ionotropic glutamate receptor family and play critical roles in the regulation of synaptic networks. The kainate receptor subunit GluK3 has unique functional ...Kainate receptors belong to the ionotropic glutamate receptor family and play critical roles in the regulation of synaptic networks. The kainate receptor subunit GluK3 has unique functional properties and contributes to presynaptic facilitation at the hippocampal mossy fiber synapses along with roles at the post-synapses. To gain structural insights into the unique functional properties and dynamics of GluK3 receptor, we imaged them via electron microscopy in the apo-state and in complex with either agonist kainate or antagonist UBP301. Our analysis of all the GluK3 full-length structures not only provides insights into the receptor transitions between desensitized and closed states but also reveals a "non-classical" conformation of neurotransmitter binding domain in the closed-state distinct from that observed in AMPA and other kainate receptor structures. We show by molecular dynamics simulations that Asp759 influences the stability of the LBD dimers and hence could be responsible for the observed conformational variability and dynamics of the GluK3 via electron microscopy. Lower dimer stability could explain faster desensitization and low agonist sensitivity of GluK3. In overview, our work helps to associate biochemistry and physiology of GluK3 receptors with their structural biology and offers structural insights into the unique functional properties of these atypical receptors.
History
DepositionOct 28, 2019-
Header (metadata) releaseMar 4, 2020-
Map releaseMar 4, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.936
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.936
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l6f
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6l6f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0839.png

Downloads & links

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Map

FileDownload / File: emd_0839.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined and sharped map
Voxel sizeX=Y=Z: 1.27 Å
Density
Contour LevelBy AUTHOR: 0.936 / Movie #1: 0.936
Minimum - Maximum-1.2299354 - 3.2463331
Average (Standard dev.)0.009627545 (±0.19624417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 419.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z419.100419.100419.100
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-1.2303.2460.010

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Supplemental data

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Half map: half map B

Fileemd_0839_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_0839_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GluK3 complex with agonist Kainate

EntireName: GluK3 complex with agonist Kainate
Components
  • Complex: GluK3 complex with agonist Kainate
    • Protein or peptide: Glutamate receptor ionotropic, kainate 3

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Supramolecule #1: GluK3 complex with agonist Kainate

SupramoleculeName: GluK3 complex with agonist Kainate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 GnTi- / Recombinant plasmid: pEGBacMam

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Macromolecule #1: Glutamate receptor ionotropic, kainate 3

MacromoleculeName: Glutamate receptor ionotropic, kainate 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 93.984922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPHVIRIGGI FEYADGPNAQ VMNAEEHAFR FSANIINRNR TLLPNTTLTY DIQRIHFHDS FEATKKACDQ LALGVVAIFG PSQGSTTNA VQSICNALEV PHIQLRWKHH PLDNKDTFYV NLYPDYASLS HAILDLVQSL KWRSATVVYD DSTGLIRLQE L IMAPSRYN ...String:
MPHVIRIGGI FEYADGPNAQ VMNAEEHAFR FSANIINRNR TLLPNTTLTY DIQRIHFHDS FEATKKACDQ LALGVVAIFG PSQGSTTNA VQSICNALEV PHIQLRWKHH PLDNKDTFYV NLYPDYASLS HAILDLVQSL KWRSATVVYD DSTGLIRLQE L IMAPSRYN IRLKIRQLPI DSDDSRPLLK EMKRGREFRI IFDCSHTMAA QILKQAMAMG MMTEYYHFIF TTLDLYALDL EP YRYSGVN LTGFRILNVD NPHVSAIVEK WSMERLQAAP RAESGLLDGV MMTDAALLYD AVHIVSVTYQ RAPQMTVNSL QCH RHKAWR FGGRFMNFIK EAQWEGLTGR IVFNKTSGLR TDFDLDIISL KEDGLEKVGV WSPADGLNIT EVAKGRGPNV TDSL TNRSL IVTTLLEEPF VMFRKSDRTL YGNDRFEGYC IDLLKELAHI LGFSYEIRLV EDGKYGAQDD KGQWNGMVKE LIDHK ADLA VAPLTITHVR EKAIDFSKPF MTLGVSILYR KPNGTNPSVF SFLNPLSPDI WMYVLLAYLG VSVVLFVIAR FSPYEW YDA HPCNPGSEVV ENNFTLLNSF WFGMGSLMQQ GSELMPKALS TRIIGGIWWF FTLIIISSYT ANLAAFLTVE RMESPID SA DDLAKQTKIE YGAVKDGATM TFFKKSKIST FEKMWAFMSS KPSALVKNNE EGIQRTLTAD YALLMESTTI EYITQRNC N LTQIGGLIDS KGYGIGTPMG SPYRDKITIA ILQLQEEDKL HIMKEKWWRG SGCPEEENKE ASALGIQKIG GIFIVLAAG LVLSVLVAVG EFIYKLRKTA EREQRSGLVP RG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 8 / Component - Concentration: 1.7 1.7 / Component - Formula: NaClSodium chloride / Component - Name: Sodium Chloride / Details: 20 mM Tris pH 8.0, 150 mM NaCl
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Details: Multiple application, blotted for 3 seconds.

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number real images: 2845 / Average electron dose: 16.73 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 46106
CTF correctionSoftware - Name: Gctf (ver. v1.06)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jfy

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v1) / Number images used: 27997

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Atomic model buiding 1

Initial modelPDB ID:

6jfy

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6l6f:
GluK3 receptor complex with UBP301

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