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- EMDB-29929: Domoate-bound GluK2 kainate receptors in non-active conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-29929
TitleDomoate-bound GluK2 kainate receptors in non-active conformation
Map dataDomoate-bound GluK2 kainate receptors in non-active conformation
Sample
  • Complex: Homotetrameric GluK2 bound with DOQ state 4
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
  • Ligand: alpha-D-mannopyranose
Keywordsion channel / glutamate kainate receptor 2 / homotetramer / MEMBRANE 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 / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade ...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 / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / 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 / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / 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 / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / neuron apoptotic process / scaffold protein binding / perikaryon / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / ubiquitin protein ligase binding / dendrite / synapse / 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: 3.93 Å
AuthorsBogdanovic N / Tajima N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM147266-01 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis of GluK2 kainate receptor activation by a partial agonist.
Authors: Guadalupe Segura-Covarrubias / Changping Zhou / Nebojša Bogdanović / Lisa Zhang / Nami Tajima /
Abstract: Kainate receptors (KARs) belong to the family of ionotropic glutamate receptors that regulate neurotransmitter release and excitatory synaptic transmission in the central nervous system. Despite ...Kainate receptors (KARs) belong to the family of ionotropic glutamate receptors that regulate neurotransmitter release and excitatory synaptic transmission in the central nervous system. Despite their critical roles in synaptic signaling and disease, the detailed gating mechanisms of KARs are not completely understood. Here we present cryo-electron microscopy structures of homomeric rat GluK2 KAR in an unliganded apo state and in complexes with a partial agonist, domoate. Partial agonist-bound GluK2 populates multiple conformations, including intermediate and desensitized states. Moreover, we demonstrate that the N-glycans at the amino-terminal domain-ligand binding domain (LBD) interface modulate receptor gating properties by interfering with cation binding at the LBD dimer interface. Together, these results provide insights into the unique gating mechanisms of KARs.
History
DepositionMar 1, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29929.png

Downloads & links

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Map

FileDownload / File: emd_29929.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDomoate-bound GluK2 kainate receptors in non-active conformation
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0138
Minimum - Maximum-0.010505458 - 0.04519585
Average (Standard dev.)0.00005800351 (±0.0014254275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29929_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_29929_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_29929_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetrameric GluK2 bound with DOQ state 4

EntireName: Homotetrameric GluK2 bound with DOQ state 4
Components
  • Complex: Homotetrameric GluK2 bound with DOQ state 4
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Homotetrameric GluK2 bound with DOQ state 4

SupramoleculeName: Homotetrameric GluK2 bound with DOQ state 4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Tetramer isolated and dyalised extensively. The DOQ was applied prior to grid freezing.
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: 98.883469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HVLRFGGIFE YVESGPMGAE ELAFRFAVNT INRNRTLLPN TTLTYDTQKI NLYDSFEASK KACDQLSLGV AAIFGPSHSS SANAVQSIC NALGVPHIQT RWKHQVSDNK DSFYVSLYPD FSSLSRAILD LVQFFKWKTV TVVYDDSTGL IRLQELIKAP S RYNLRLKI ...String:
HVLRFGGIFE YVESGPMGAE ELAFRFAVNT INRNRTLLPN TTLTYDTQKI NLYDSFEASK KACDQLSLGV AAIFGPSHSS SANAVQSIC NALGVPHIQT RWKHQVSDNK DSFYVSLYPD FSSLSRAILD LVQFFKWKTV TVVYDDSTGL IRLQELIKAP S RYNLRLKI RQLPADTKDA KPLLKEMKRG KEFHVIFDCS HEMAAGILKQ ALAMGMMTEY YHYIFTTLDL FALDVEPYRY SG VNMTGFR ILNTENTQVS SIIEKWSMER LQAPPKPDSG LLDGFMTTDA ALMYDAVHVV SVAVQQFPQM TVSSLQCNRH KPW RFGTRF MSLIKEAHWE GLTGRITFNK TNGLRTDFDL DVISLKEEGL EKIGTWDPAS GLNMTESQKG KPANITDSLS NRSL IVTTI LEEPYVLFKK SDKPLYGNDR FEGYCIDLLR ELSTILGFTY EIRLVEDGKY GAQDDVNGQW NGMVRELIDH KADLA VAPL AITYVREKVI DFSKPFMTLG ISILYRKPNG TNPGVFSFLN PLSPDIWMYV LLAYLGVSVV LFVIARFSPY EWYNPH PSN PDSDVVENNF TLLNSFWFGV GALMQQGSEL MPKALSTRIV GGIWWFFTLI IISSYTANLA AFLTVERMES PIDSADD LA KQTKIEYGAV EDGATMTFFK KSKISTYDKM WAFMSSRRQS VLVKSNEEGI QRVLTSDYAF LMESTTIEFV TQRNCNLT Q IGGLIDSKGY GVGTPMGSPY RDKITIAILQ LQEEGKLHMM KEKWWRGNGC PEEESKEASA LGVQNIGGIF IVLAAGLVL SVFVAVGEFL YKSKKNAQLE KRSFCSAMVE ELRMSLKCQR RLKHKPQAPV IVKTEEVINM HTFNDRRLPG KETMA

UniProtKB: Glutamate receptor ionotropic, kainate 2

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIE...

MacromoleculeName: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
type: ligand / ID: 6 / Number of copies: 4 / Formula: DOQ
Molecular weightTheoretical: 311.33 Da
Chemical component information

ChemComp-DOQ:
(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID

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Macromolecule #7: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration3.5 mg/mL
BufferpH: 8 / Component - Concentration: 150.0 mmol / Component - Formula: NaCl / Component - Name: sodium chloride / Details: 50 mM Tris/HCl 150 mM NaCl 1mM DDM pH 8.0
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was isolated from SEC and concentrated. Monodispersity of the final sample determined by the analytical HPLC, Superose 6 increase column

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12486 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 2481151
Details: Initially picked particles that are later classified in several rounds of 2D and 3D classifications. The number of final classes for this dataset is 4 of which this state represents "class ...Details: Initially picked particles that are later classified in several rounds of 2D and 3D classifications. The number of final classes for this dataset is 4 of which this state represents "class 2" and contains 100389 as the final number of particles.
CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5kuf

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Software - details: beta / Number images used: 100389
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) / Software - details: beta
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 4.0) / Software - details: beta
Final 3D classificationNumber classes: 5 / Avg.num./class: 60000 / Software - Name: RELION (ver. 4.0) / Software - details: beta
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 70 / Target criteria: 0.85
Output model

PDB-8gc5:
Domoate-bound GluK2 kainate receptors in non-active conformation

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