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- EMDB-48896: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the... -

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Basic information

Entry
Database: EMDB / ID: EMD-48896
TitleLigand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Map dataLigand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Sample
  • Complex: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
    • Protein or peptide: Glutamate ionotropic receptor kainate type subunit 2 (GluK2)
    • Protein or peptide: Neuropilin and tolloid-like protein 2 (Neto2)
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 / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade / inhibitory postsynaptic potential / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / receptor clustering / kainate selective glutamate receptor activity / extracellularly glutamate-gated ion channel activity / modulation of excitatory postsynaptic potential / ionotropic glutamate receptor complex / positive regulation of synaptic transmission / behavioral fear response / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ionotropic glutamate receptor binding / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / hippocampal mossy fiber to CA3 synapse / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / presynaptic membrane / neuron apoptotic process / scaffold protein binding / chemical synaptic transmission / negative regulation of neuron apoptotic process / perikaryon / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / ubiquitin protein ligase binding / synapse / dendrite / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A ...CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / 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
Neuropilin and tolloid-like protein 2 / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 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: To Be Published
Title: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Authors: Gangwar SP / Yelshanskaya MV / Yen LY / Newton TP / Sobolevsky AI
History
DepositionFeb 3, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48896.png

Downloads & links

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Map

FileDownload / File: emd_48896.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLigand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033
Minimum - Maximum-0.42824036 - 0.6152105
Average (Standard dev.)0.00040890626 (±0.009201187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus map for GluK2-2xNeto2 in the open state,...

Fileemd_48896_additional_1.map
AnnotationConsensus map for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the...

Fileemd_48896_half_map_1.map
AnnotationLigand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the...

Fileemd_48896_half_map_2.map
AnnotationLigand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the...

EntireName: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
Components
  • Complex: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
    • Protein or peptide: Glutamate ionotropic receptor kainate type subunit 2 (GluK2)
    • Protein or peptide: Neuropilin and tolloid-like protein 2 (Neto2)

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Supramolecule #1: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the...

SupramoleculeName: Ligand-binding and transmembrane domains for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
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
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
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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Macromolecule #2: Neuropilin and tolloid-like protein 2 (Neto2)

MacromoleculeName: Neuropilin and tolloid-like protein 2 (Neto2) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString: MALEQLCAVL KVLLITVLVV EGIAVAQKTQ DGQNIGIKHV PATQCGIWVR TSNGGHFASP NYPDSYPPNK ECIYILEAAP RQRIELTFDE RYYIEPSFEC RFDHLEVRDG PFGFSPLIDR YCGMKSPALI RSTGRFMWIK FSSDEELEGL GFRAKYSFIP DPDFTYLGGI ...String:
MALEQLCAVL KVLLITVLVV EGIAVAQKTQ DGQNIGIKHV PATQCGIWVR TSNGGHFASP NYPDSYPPNK ECIYILEAAP RQRIELTFDE RYYIEPSFEC RFDHLEVRDG PFGFSPLIDR YCGMKSPALI RSTGRFMWIK FSSDEELEGL GFRAKYSFIP DPDFTYLGGI LNPIPDCQFE LSGADGIVRS SQVEQEEKTK PGQAVDCIWT IKATPKAKIY LRFLDYQMEH SNECKRNFVA VYDGSSAIEN LKAKFCSTVA NDVMLKTGVG VIRMWADEGS RLSRFRMLFT SFVEPPCTSS TFFCHSNMCI NNSLVCNGVQ NCAYPWDENH CKEKKKAGLF EQITKTHGTI IGVTSGIVLV LLIISILVQV KQPRKKVMAC KTAFNKTGFQ EVFDPPHYEL FSLREKEISA DLADLSEELD NYQKLRRSST ASRCIHDHHC GSQASSVKQS RTNLSSMELP FRNDFAQPQP MKTFNSTFKK SSYTFKQTHD CPEQALEDRV MEEIPCEIYV RGRDDSAQAS ISIDF

UniProtKB: Neuropilin and tolloid-like protein 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
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMSodium Chloride
0.05 %Digitonin
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: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 193705
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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