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- EMDB-8289: GluK2EM with 2S,4R-4-methylglutamate -

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Basic information

Entry
Database: EMDB / ID: EMD-8289
TitleGluK2EM with 2S,4R-4-methylglutamate
Map dataGluK2EM with 2S,4R-4-methylglutamate
Sample
  • Complex: GluK2EM with 2S,4R-4-methylglutamate
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
  • Ligand: 2S,4R-4-METHYLGLUTAMATE
KeywordsGluK2EM with 2S / 4R-4-methylglutamate / SIGNALING PROTEIN
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / regulation of JNK cascade / receptor clustering / modulation of excitatory postsynaptic potential / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / neuronal action potential / 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 / presynaptic modulation of chemical synaptic transmission / SNARE binding / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / neuron apoptotic process / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / membrane / 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 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMeyerson JR / Chittori S
CitationJournal: Nature / Year: 2016
Title: Structural basis of kainate subtype glutamate receptor desensitization.
Authors: Joel R Meyerson / Sagar Chittori / Alan Merk / Prashant Rao / Tae Hee Han / Mihaela Serpe / Mark L Mayer / Sriram Subramaniam /
Abstract: Glutamate receptors are ligand-gated tetrameric ion channels that mediate synaptic transmission in the central nervous system. They are instrumental in vertebrate cognition and their dysfunction ...Glutamate receptors are ligand-gated tetrameric ion channels that mediate synaptic transmission in the central nervous system. They are instrumental in vertebrate cognition and their dysfunction underlies diverse diseases. In both the resting and desensitized states of AMPA and kainate receptor subtypes, the ion channels are closed, whereas the ligand-binding domains, which are physically coupled to the channels, adopt markedly different conformations. Without an atomic model for the desensitized state, it is not possible to address a central problem in receptor gating: how the resting and desensitized receptor states both display closed ion channels, although they have major differences in the quaternary structure of the ligand-binding domain. Here, by determining the structure of the kainate receptor GluK2 subtype in its desensitized state by cryo-electron microscopy (cryo-EM) at 3.8 Å resolution, we show that desensitization is characterized by the establishment of a ring-like structure in the ligand-binding domain layer of the receptor. Formation of this 'desensitization ring' is mediated by staggered helix contacts between adjacent subunits, which leads to a pseudo-four-fold symmetric arrangement of the ligand-binding domains, illustrating subtle changes in symmetry that are important for the gating mechanism. Disruption of the desensitization ring is probably the key switch that enables restoration of the receptor to its resting state, thereby completing the gating cycle.
History
DepositionJul 13, 2016-
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 2016-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.047
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.047
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5kuf
  • Surface level: 0.047
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8289.png

Downloads & links

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Map

FileDownload / File: emd_8289.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK2EM with 2S,4R-4-methylglutamate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 300 pix.
= 397.2 Å		1.32 Å/pix.
x 300 pix.
= 397.2 Å		1.32 Å/pix.
x 300 pix.
= 397.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.324 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.037 / Movie #1: 0.047
Minimum - Maximum-0.07969753 - 0.16108571
Average (Standard dev.)-0.0000018445252 (±0.006908057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 397.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3241.3241.324
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z397.200397.200397.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0800.161-0.000

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Supplemental data

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Sample components

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Entire : GluK2EM with 2S,4R-4-methylglutamate

EntireName: GluK2EM with 2S,4R-4-methylglutamate
Components
  • Complex: GluK2EM with 2S,4R-4-methylglutamate
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
  • Ligand: 2S,4R-4-METHYLGLUTAMATE

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Supramolecule #1: GluK2EM with 2S,4R-4-methylglutamate

SupramoleculeName: GluK2EM with 2S,4R-4-methylglutamate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate receptor ionotropic, kainate 2

MacromoleculeName: Glutamate receptor ionotropic, kainate 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 99.086719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TTHVLRFGGI FEYVESGPMG AEELAFRFAV NTINRNRTLL PNTTLTYDTQ KINLYDSFEA SKKACDQLSL GVAAIFGPSH SSSANAVQS ICNALGVPHI QTRWKHQVSD NKDSFYVSLY PDFSSLSRAI LDLVQFFKWK TVTVVYDDST GLIRLQELIK A PSRYNLRL ...String:
TTHVLRFGGI FEYVESGPMG AEELAFRFAV NTINRNRTLL PNTTLTYDTQ KINLYDSFEA SKKACDQLSL GVAAIFGPSH SSSANAVQS ICNALGVPHI QTRWKHQVSD NKDSFYVSLY PDFSSLSRAI LDLVQFFKWK TVTVVYDDST GLIRLQELIK A PSRYNLRL KIRQLPADTK DAKPLLKEMK RGKEFHVIFD CSHEMAAGIL KQALAMGMMT EYYHYIFTTL DLFALDVEPY RY SGVNMTG FRILNTENTQ VSSIIEKWSM ERLQAPPKPD SGLLDGFMTT DAALMYDAVH VVSVAVQQFP QMTVSSLQCN RHK PWRFGT RFMSLIKEAH WEGLTGRITF NKTNGLRTDF DLDVISLKEE GLEKIGTWDP ASGLNMTESQ KGKPANITDS LSNR SLIVT TILEEPYVLF KKSDKPLYGN DRFEGYCIDL LRELSTILGF TYEIRLVEDG KYGAQDDVNG QWNGMVRELI DHKAD LAVA PLTITYVREK VIDFSKPFMT LGISILYRKP NGTNPGVFSF LNPLSPDIWM YVLLAYLGVS VVLFVIARFS PYEWYN PHP CNPDSDVVEN NFTLLNSFWF GVGALMQQGS ELMPKALSTR IVGGIWWFFT LIIISSYTAN LAAFLTVERM ESPIDSA DD LAKQTKIEYG AVEDGSTMTF FKKSKISTYD KMWAFMSSRR QSVLVKSSEE GIQRVLTSDY ALLMESTTIE FVTQRNCN L TQIGGLIDSK GYGVGTPMGS PYRDKITIAI LQLQEEGKLH MMKEKWWRGN GCPEEESKEA SALGVQNIGG IFIVLAAGL VLSVFVAVGE FLYKSKKNAQ LEKRSFCSAM VEELRMSLKC QRRLKHKPQA PVIVKTEEVI NMHTFNDRRL PGKETMA

UniProtKB: Glutamate receptor ionotropic, kainate 2

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Macromolecule #2: 2S,4R-4-METHYLGLUTAMATE

MacromoleculeName: 2S,4R-4-METHYLGLUTAMATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: SYM
Molecular weightTheoretical: 160.148 Da
Chemical component information

ChemComp-SYM:
2S,4R-4-METHYLGLUTAMATE

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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

Concentration4.2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE
DetailsGluK2

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND3 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 62244
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.3)

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