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- EMDB-9821: GluK3 receptor trapped in Desensitized state -

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Basic information

Entry
Database: EMDB / ID: EMD-9821
TitleGluK3 receptor trapped in Desensitized state
Map data
Sample
  • Complex: GluK3 complex with agonist SYM
    • Protein or peptide: Glutamate receptor ionotropic, kainate 3
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / 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 / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / monoatomic ion transmembrane transport / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / glutamatergic synapse / dendrite / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsKumari J / Kumar J
Funding support India, 2 items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/501023 India
Department of Biotechnology (India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: Sci Rep / Year: 2019
Title: Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery.
Authors: Jyoti Kumari / Rajesh Vinnakota / Janesh Kumar /
Abstract: GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better ...GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. While the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a resting state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using structures as a guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. The mutational analysis also identified putative N-glycan interacting residues. Our results provide a molecular framework for understanding gating properties unique to GluK3 and exploring the role of N-linked glycosylation in their modulation.
History
DepositionFeb 13, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.863
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.863
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jfy
  • Surface level: 0.863
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9821.png

Downloads & links

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Map

FileDownload / File: emd_9821.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 300 pix.
= 414. Å		1.38 Å/pix.
x 300 pix.
= 414. Å		1.38 Å/pix.
x 300 pix.
= 414. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.863 / Movie #1: 0.863
Minimum - Maximum-2.0578704 - 3.3673804
Average (Standard dev.)0.0043503027 (±0.1422088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-2.0583.3670.004

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Supplemental data

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Half map: Half map A

Fileemd_9821_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_9821_half_map_2.map
AnnotationHalf map B
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 SYM

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

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Supramolecule #1: GluK3 complex with agonist SYM

SupramoleculeName: GluK3 complex with agonist SYM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 / Recombinant plasmid: pEG BacMAM
Molecular weightTheoretical: 400 KDa

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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: 91.305812 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 LVLSVLVAV

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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:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClSodium chloride
0.75 mMDDMDDM
0.03 mMCHScholesterol hemisuccinate
VitrificationCryogen name: ETHANE
DetailsPurified and detergent solubilized GluK3 receptors

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 719 / Average exposure time: 60.0 sec. / Average electron dose: 16.73 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware:
Namedetails
GctfgCTF was used for estimation
cryoSPARC (ver. 1)CTF correction
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3olz


Details: 3OLZ (ATD), XXXX(LBD), 5KUF(TM)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1) / Software - details: final reconstruction / Number images used: 9730
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 1) / Software - details: Abinitio 3D reconstruction / Details: Abinitio 3D reconstruction module of cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 1) / Software - details: cryoSPARC / Details: CryoSPARC
Final 3D classificationNumber classes: 2

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6jfy:
GluK3 receptor trapped in Desensitized state

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