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- EMDB-70807: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-met... -

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Entry
Database: EMDB / ID: EMD-70807
TitleThe intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Map dataThe intact LBD state of GluK2/K5 bound to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Sample
  • Complex: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
    • Protein or peptide: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
KeywordsKainate receptor / ionotropic glutamate receptor / membrane protein / ligand-gated ion channel / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / 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 ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / 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 / 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 / establishment of localization in cell / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / bioluminescence / hippocampal mossy fiber to CA3 synapse / SNARE binding / generation of precursor metabolites and energy / PDZ domain binding / synaptic transmission, glutamatergic / excitatory postsynaptic potential / cellular response to glucose stimulus / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / intracellular protein transport / SH3 domain binding / 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 / neuron apoptotic process / presynaptic membrane / 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 / endoplasmic reticulum / nucleoplasm / membrane / identical protein binding / plasma membrane
Similarity search - Function
Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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 / : ...Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Green fluorescent protein / Glutamate receptor ionotropic, kainate 2 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsKhanra NK / Meyerson JR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1 R35 GM142662 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structures of partially occupied hetero-tetramers provide insight into kainate receptor activation and desensitization.
Authors: Nandish K Khanra / Alexa Strauss / Laura Moreno Wasielewski / Sophie Lenze / Joel Meyerson / Andreas Reiner / Joshua Levitz /
Abstract: Kainate receptors (KARs) are critical mediators and modulators of synaptic transmission which undergo rapid activation and desensitization upon binding of the neurotransmitter glutamate. Under ...Kainate receptors (KARs) are critical mediators and modulators of synaptic transmission which undergo rapid activation and desensitization upon binding of the neurotransmitter glutamate. Under various physiological and pharmacological conditions agonist binding likely occurs to only a subset of subunits within these tetrameric receptors, motivating an analysis of the functional and conformational effects of partial versus complete ligand occupancy. Here we report cryo-EM structures of the GluK2/GluK5 hetero-tetramer under partially-occupied conditions using 5-iodowillardiine and AMPA as GluK5-selective agonists. High-resolution pre-active state structures containing closed/open ligand binding domain (LBD) dimers with intact interfaces reveal gating-associated interface reshaping, inter-dimer motions, and pore-linker repositioning in response to asymmetric agonist binding. Interfacial LBD mutations to a central cluster formed by the GluK5 subunits and to an inter-dimer interface between GluK2 and GluK5 subunits, highlight the roles of interactions between LBD dimers in controlling receptor function, including the distinct slow deactivation of GluK5-containing receptors. Finally, the absence or presence of intact, partially, and fully ruptured LBD interfaces under different ligand conditions allows us to propose a revised model of stepwise ionotropic glutamate receptor activation and desensitization.
History
DepositionMay 24, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70807.png

Downloads & links

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Map

FileDownload / File: emd_70807.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe intact LBD state of GluK2/K5 bound to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 416 pix.
= 450.528 Å		1.08 Å/pix.
x 416 pix.
= 450.528 Å		1.08 Å/pix.
x 416 pix.
= 450.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-1.6862351 - 2.7181346
Average (Standard dev.)0.0013099692 (±0.042201534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 450.52798 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The amino terminal domain (ATD) of the intact...

Fileemd_70807_additional_1.map
AnnotationThe amino terminal domain (ATD) of the intact LBD state of GluK2/K5 bound to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The ligand binding and transmembrane domain (LBD-TMD) of...

Fileemd_70807_additional_2.map
AnnotationThe ligand binding and transmembrane domain (LBD-TMD) of the intact LBD state of GluK2/K5 bound to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the intact LBD state...

Fileemd_70807_half_map_1.map
AnnotationHalf map 1 of the intact LBD state of GluK2/K5 bound to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the intact LBD state...

Fileemd_70807_half_map_2.map
AnnotationHalf map 2 of the intact LBD state of GluK2/K5 bound to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-met...

EntireName: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Components
  • Complex: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
    • Protein or peptide: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2

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Supramolecule #1: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-met...

SupramoleculeName: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 458.802 KDa

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Macromolecule #1: Glutamate receptor ionotropic, kainate 5,Green fluorescent protei...

MacromoleculeName: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
type: protein_or_peptide / ID: 1
Details: Glutamate receptor ionotropic, kainate 5 with Green fluorescent protein at the C-terminal
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 123.676812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPAELLLLLI VAFANPSCQV LSSLRMAAIL DDQTVCGRGE RLALALAREQ INGIIEVPAK ARVEVDIFEL QRDSQYETTD TMCQILPKG VVSVLGPSSS PASASTVSHI CGEKEIPHIK VGPEETPRLQ YLRFASVSLY PSNEDVSLAV SRILKSFNYP S ASLICAKA ...String:
MPAELLLLLI VAFANPSCQV LSSLRMAAIL DDQTVCGRGE RLALALAREQ INGIIEVPAK ARVEVDIFEL QRDSQYETTD TMCQILPKG VVSVLGPSSS PASASTVSHI CGEKEIPHIK VGPEETPRLQ YLRFASVSLY PSNEDVSLAV SRILKSFNYP S ASLICAKA ECLLRLEELV RGFLISKETL SVRMLDDSRD PTPLLKEIRD DKVSTIIIDA NASISHLVLR KASELGMTSA FY KYILTTM DFPILHLDGI VEDSSNILGF SMFNTSHPFY PEFVRSLNMS WRENCEASTY PGPALSAALM FDAVHVVVSA VRE LNRSQE IGVKPLACTS ANIWPHGTSL MNYLRMVEYD GLTGRVEFNS KGQRTNYTLR ILEKSRQGHR EIGVWYSNRT LAMN ATTLD INLSQTLANK TLVVTTILEN PYVMRRPNFQ ALSGNERFEG FCVDMLRELA ELLRFRYRLR LVEDGLYGAP EPNGS WTGM VGELINRKAD LAVAAFTITA EREKVIDFSK PFMTLGISIL YRVHMGRKPG YFSFLDPFSP AVWLFMLLAY LAVSVV LFL AARLSPYEWY NPHPSLRARP HILENQYTLG NSLWFPVGGF MQQGSEIMPR ALSTRIVSGV WWAFTLIIIS SYTANLA AF LTVQRMEVPV ESADDLADQT NIEYGTIHAG STMTFFQNSR YQTYQRMWNY MQSKQPSVFV KSTEEGIARV LNSRYAFL L ESTMNEYHRR LNCNLTQIGG LLDTKGYGIG MPLGSPFRDE ITLAILQLQE NNRLEILKRK WWEGGRCPKE EDHRAKGLG MENIGGIFVV LIAGLIIAVF VAVMEFIYKS RAEAKRMKGL VPRGSAAAAM VSKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAMP EGYVQERTIF FKDDGNYKTR A EVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK NGIKVNFKIR HNIEDGSVQL ADHYQQNTPI GD GPVLLPD NHYLSTQSKL SKDPNEKRDH MVLLEFVTAA GITLGMDELY KSGLRTETSQ VAPA

UniProtKB: Glutamate receptor ionotropic, kainate 5, Green fluorescent protein

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Macromolecule #2: Glutamate receptor ionotropic, kainate 2

MacromoleculeName: Glutamate receptor ionotropic, kainate 2 / type: protein_or_peptide / ID: 2 / Details: Glutamate receptor ionotropic, kainate 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 105.981617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSF EASKKACDQL SLGVAAIFGP SHSSSANAVQ SICNALGVPH IQTRWKHQVS DNKDSFYVSL YPDFSSLSRA I LDLVQFFK ...String:
MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSF EASKKACDQL SLGVAAIFGP SHSSSANAVQ SICNALGVPH IQTRWKHQVS DNKDSFYVSL YPDFSSLSRA I LDLVQFFK WKTVTVVYDD STGLIRLQEL IKAPSRYNLR LKIRQLPADT KDAKPLLKEM KRGKEFHVIF DCSHEMAAGI LK QALAMGM MTEYYHYIFT TLDLFALDVE PYRYSGVNMT GFRILNTENT QVSSIIEKWS MERLQAPPKP DSGLLDGFMT TDA ALMYDA VHVVSVAVQQ FPQMTVSSLQ CNRHKPWRFG TRFMSLIKEA HWEGLTGRIT FNKTNGLRTD FDLDVISLKE EGLE KIGTW DPASGLNMTE SQKGKPANIT DSLSNRSLIV TTILEEPYVL FKKSDKPLYG NDRFEGYCID LLRELSTILG FTYEI RLVE DGKYGAQDDV NGQWNGMVRE LIDHKADLAV APLAITYVRE KVIDFSKPFM TLGISILYRK PNGTNPGVFS FLNPLS PDI WMYVLLAYLG VSVVLFVIAR FSPYEWYNPH PSNPDSDVVE NNFTLLNSFW FGVGALMQQG SELMPKALST RIVGGIW WF FTLIIISSYT ANLAAFLTVE RMESPIDSAD DLAKQTKIEY GAVEDGATMT FFKKSKISTY DKMWAFMSSR RQSVLVKS N EEGIQRVLTS DYAFLMESTT IEFVTQRNCN LTQIGGLIDS KGYGVGTPMG SPYRDKITIA ILQLQEEGKL HMMKEKWWR GNGCPEEESK EASALGVQNI GGIFIVLAAG LVLSVFVAVG EFLYKSKKNA QLEKRSFCSA MVEELRMSLK CQRRLKHKPQ APVIVKTEE VINMHTFNDR RLPGKETMAS GLRSAWSHPQ FEKGGGSGGG SGGGSWSHPQ FEK

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

Concentration3.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTris
300.0 mMNaClNaCl
0.35 mMn-Dodecyl-beta-D-MaltopyranosideDDM

Details: 20 mM Tris, 300 mM NaCl, 0.35 mM DDM, pH 8.0
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: Functionalized with PEG-thiol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.28 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7403033
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction in CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 189632
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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