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- EMDB-49070: Consensus map for GluK2-2xNeto2 in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-49070
TitleConsensus map for GluK2-2xNeto2 in the apo state
Map dataConsensus map for GluK2-2xNeto2 in the apo state
Sample
  • Complex: Consensus map for GluK2-2xNeto2 in the apo state
    • 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 / 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 / neurotransmitter receptor localization to postsynaptic specialization membrane / receptor clustering / glutamate receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / ionotropic glutamate receptor binding / 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
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 / 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
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: 3.89 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: Consensus map for GluK2-2xNeto2 in the apo state
Authors: Gangwar SP / Yelshanskaya MV / Yen LY / Newton TP / Sobolevsky AI
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49070.png

Downloads & links

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Map

FileDownload / File: emd_49070.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map for GluK2-2xNeto2 in the apo state
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: 0.035
Minimum - Maximum-0.10685861 - 0.18161646
Average (Standard dev.)0.00043365458 (±0.005972024)
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 GluK2-2xNeto2 in the apo state

Fileemd_49070_half_map_1.map
AnnotationConsensus map for GluK2-2xNeto2 in the apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus map for GluK2-2xNeto2 in the apo state

Fileemd_49070_half_map_2.map
AnnotationConsensus map for GluK2-2xNeto2 in the apo state
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 GluK2-2xNeto2 in the apo state

EntireName: Consensus map for GluK2-2xNeto2 in the apo state
Components
  • Complex: Consensus map for GluK2-2xNeto2 in the apo state
    • 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: Consensus map for GluK2-2xNeto2 in the apo state

SupramoleculeName: Consensus map for GluK2-2xNeto2 in the apo state / 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)
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
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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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