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- EMDB-49068: Consensus map for GluK2-0xNeto2 in the apo state with asymmetric ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49068
TitleConsensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
Map dataConsensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
Sample
  • Complex: Consensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
    • Protein or peptide: Glutamate ionotropic receptor kainate type subunit 2 (GluK2)
KeywordsKainate receptor / GluK2 / Ion Channel / Neto2 / MEMBRANE PROTEIN
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / regulation of short-term neuronal synaptic plasticity / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade / glutamate receptor activity ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / regulation of short-term neuronal synaptic plasticity / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade / glutamate receptor activity / inhibitory postsynaptic potential / behavioral fear response / receptor clustering / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / neuronal action potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / modulation of excitatory postsynaptic potential / neuron apoptotic process / positive regulation of synaptic transmission / regulation of long-term neuronal synaptic plasticity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / intracellular protein transport / postsynaptic density membrane / intracellular calcium ion homeostasis / modulation of chemical synaptic transmission / positive regulation of neuron apoptotic process / terminal bouton / negative regulation of neuron apoptotic process / scaffold protein binding / presynaptic membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / postsynaptic density / axon / ubiquitin protein ligase binding / neuronal cell body / synapse / dendrite / glutamatergic synapse / membrane / identical protein binding / 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 ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsGangwar SP / Yelshanskaya MV / Yen LY / Newton TP / Sobolevsky AI
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS107253 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR078814 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA206573 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21 NS139087 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Activation of kainate receptor GluK2-Neto2 complex.
Authors: Shanti Pal Gangwar / Maria V Yelshanskaya / Laura Y Yen / Thomas P Newton / Alexander I Sobolevsky /
Abstract: Kainate receptors (KARs) are tetrameric, ligand-gated ion channels of the ionotropic glutamate receptor family that mediate excitatory neurotransmission and modulate neuronal circuits and synaptic ...Kainate receptors (KARs) are tetrameric, ligand-gated ion channels of the ionotropic glutamate receptor family that mediate excitatory neurotransmission and modulate neuronal circuits and synaptic plasticity during development of the central nervous system. KARs are implicated in psychiatric and neurological diseases and represent a target of therapeutic intervention. Native KARs form complexes with neuropilin and tolloid-like auxiliary subunits (Neto1 and Neto2), which modulate their function, trafficking and synaptic localization. Here we present structures of rat GluK2 KAR in the apo closed state and in the open states activated by agonist kainate and positive allosteric modulator BPAM344, solved in the presence and absence of Neto2 using time-resolved cryo-electron microscopy. While the binding of Neto2 does not change the behavior of individual or dimeric ligand-binding domains (LBDs) or the ion channel, it prevents tightening of the interface between two LBD dimers during activation and slows the kinetics of deactivation. Our structures illuminate the mechanism of KAR activation and its modulation by Neto2.
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49068.png

Downloads & links

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Map

FileDownload / File: emd_49068.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.33803475 - 0.5407318
Average (Standard dev.)0.00093385036 (±0.014763433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Consensus map for GluK2-0xNeto2 in the apo state...

Fileemd_49068_half_map_1.map
AnnotationConsensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus map for GluK2-0xNeto2 in the apo state...

Fileemd_49068_half_map_2.map
AnnotationConsensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Consensus map for GluK2-0xNeto2 in the apo state with asymmetric ...

EntireName: Consensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
Components
  • Complex: Consensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
    • Protein or peptide: Glutamate ionotropic receptor kainate type subunit 2 (GluK2)

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Supramolecule #1: Consensus map for GluK2-0xNeto2 in the apo state with asymmetric ...

SupramoleculeName: Consensus map for GluK2-0xNeto2 in the apo state with asymmetric ligand-binding domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate ionotropic receptor kainate type subunit 2 (GluK2)

MacromoleculeName: Glutamate ionotropic receptor kainate type subunit 2 (GluK2)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSFE ASKKACDQLS LGVAAIFGPS HSSSANAVQS ICNALGVPHI QTRWKHQVSD NKDSFYVSLY PDFSSLSRAI LDLVQFFKWK ...String:
MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSFE ASKKACDQLS LGVAAIFGPS HSSSANAVQS ICNALGVPHI QTRWKHQVSD NKDSFYVSLY PDFSSLSRAI LDLVQFFKWK TVTVVYDDST GLIRLQELIK APSRYNLRLK IRQLPADTKD AKPLLKEMKR GKEFHVIFDC SHEMAAGILK QALAMGMMTE YYHYIFTTLD LFALDVEPYR YSGVNMTGFR ILNTENTQVS SIIEKWSMER LQAPPKPDSG LLDGFMTTDA ALMYDAVHVV SVAVQQFPQM TVSSLQCNRH KPWRFGTRFM SLIKEAHWEG LTGRITFNKT NGLRTDFDLD VISLKEEGLE KIGTWDPASG LNMTESQKGK PANITDSLSN RSLIVTTILE EPYVLFKKSD KPLYGNDRFE GYCIDLLREL STILGFTYEI RLVEDGKYGA QDDVNGQWNG MVRELIDHKA DLAVAPLAIT YVREKVIDFS KPFMTLGISI LYRKPNGTNP GVFSFLNPLS PDIWMYVLLA CLGVSCVLFV IARFSPYEWY NPHPCNPDSD VVENNFTLLN SFWFGVGALM QQGSELMPKA LSTRIVGGIW WFFTLIIISS YTANLAAFLT VERMESPIDS ADDLAKQTKI EYGAVEDGAT MTFFKKSKIS TYDKMWAFMS SRRQSVLVKS NEEGIQRVLT SDYAFLMEST TIEFVTQRNC NLTQIGGLID SKGYGVGTPM GSPYRDKITI AILQLQEEGK LHMMKEKWWR GNGCPEEESK EASALGVQNI GGIFIVLAAG LVLSVFVAVG EFLYKSKKNA QLEKRSFCSA MVEELRMSLK CQRRLKHKPQ APVIVKTEEV INMHTFNDRR LPGKETMA

UniProtKB: Glutamate receptor ionotropic, kainate 2

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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