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- EMDB-76055: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD) -

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Basic information

Entry
Database: EMDB / ID: EMD-76055
TitleGluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD)
Map dataA2y5CNIH1 open
Sample
  • Complex: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD)
    • Protein or peptide: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
    • Protein or peptide: Protein cornichon homolog 1
  • Ligand: GLUTAMIC ACID
  • Ligand: N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide
Keywordsionotropic glutamate receptor (iGluR) / GluA2 / transmembrane AMPAR regulatory protein (TARP) / y5 / cornichon / CNIH1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


postsynaptic neurotransmitter receptor diffusion trapping / Cargo concentration in the ER / regulation of AMPA receptor activity / channel regulator activity / COPII-mediated vesicle transport / regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head ...postsynaptic neurotransmitter receptor diffusion trapping / Cargo concentration in the ER / regulation of AMPA receptor activity / channel regulator activity / COPII-mediated vesicle transport / regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / regulation of receptor recycling / kainate selective glutamate receptor activity / transmission of nerve impulse / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / cellular response to glycine / immunoglobulin binding / asymmetric synapse / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / conditioned place preference / regulation of synaptic transmission, glutamatergic / vesicle-mediated transport / response to fungicide / voltage-gated calcium channel activity / cytoskeletal protein binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of synaptic transmission, glutamatergic / regulation of long-term synaptic depression / endoplasmic reticulum-Golgi intermediate compartment membrane / glutamate-gated calcium ion channel activity / somatodendritic compartment / presynaptic active zone membrane / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / excitatory synapse / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / positive regulation of excitatory postsynaptic potential / dendritic shaft / SNARE binding / synaptic membrane / establishment of protein localization / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / ER to Golgi transport vesicle membrane / long-term synaptic potentiation / receptor internalization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / presynapse / synaptic vesicle / amyloid-beta binding / signaling receptor activity / growth cone / scaffold protein binding / chemical synaptic transmission / presynaptic membrane / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / immune response / external side of plasma membrane / Golgi membrane / signaling receptor binding / axon / neuronal cell body / dendrite / protein kinase binding / endoplasmic reticulum membrane / synapse / protein-containing complex binding / glutamatergic synapse / cell surface / signal transduction / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding
Similarity search - Function
Voltage-dependent calcium channel, gamma-5 subunit / PMP-22/EMP/MP20/Claudin tight junction / Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / : / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily ...Voltage-dependent calcium channel, gamma-5 subunit / PMP-22/EMP/MP20/Claudin tight junction / Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / : / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin 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
Protein cornichon homolog 1 / Glutamate receptor 2 / Voltage-dependent calcium channel gamma-5 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsGangwar SP / Newton TP / Yen LY / Sobolevsky AI
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS139087 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS147755 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS132554 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS107253 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR078814 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206573 United States
CitationJournal: Nat Commun / Year: 2026
Title: Tuning of AMPA receptor activation by inhibitory auxiliary subunits and epilepsy-associated disease mutations
Authors: Newton TP / Yelshanskaya MV / Aktolun M / Gangwar SP / Yen LY / Alekseev AA / Sobolevsky IA / Kurnikova MG / Sobolevsky AI
History
DepositionMar 13, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76055.png

Downloads & links

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Map

FileDownload / File: emd_76055.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA2y5CNIH1 open
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 416 pix.
= 345.28 Å		0.83 Å/pix.
x 416 pix.
= 345.28 Å		0.83 Å/pix.
x 416 pix.
= 345.28 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: 0.1
Minimum - Maximum-0.47754276 - 0.82929814
Average (Standard dev.)0.0005353921 (±0.01659751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 345.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map b

Fileemd_76055_half_map_1.map
Annotationhalf map b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map a

Fileemd_76055_half_map_2.map
Annotationhalf map a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD)

EntireName: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD)
Components
  • Complex: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD)
    • Protein or peptide: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
    • Protein or peptide: Protein cornichon homolog 1
  • Ligand: GLUTAMIC ACID
  • Ligand: N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide

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Supramolecule #1: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD)

SupramoleculeName: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium ch...

MacromoleculeName: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
type: protein_or_peptide / ID: 1
Details: rat GluA2 covalently fused to rat TARP y5,rat GluA2 covalently fused to rat TARP y5
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 117.489977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA ...String:
MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA AEKKWQVTAI NVGNINNDKK DETYRSLFQD LELKKERRVI LDCERDKVND IVDQVITIGK HVKGYHYIIA NL GFTDGDL LKIQFGGAEV SGFQIVDYDD SLVSKFIERW STLEEKEYPG AHTATIKYTS ALTYDAVQVM TEAFRNLRKQ RIE ISRRGN AGDCLANPAV PWGQGVEIER ALKQVQVEGL SGNIKFDQNG KRINYTINIM ELKTNGPRKI GYWSEVDKMV LTED DTSGL EQKTVVVTTI LESPYVMMKK NHEMLEGNER YEGYCVDLAA EIAKHCGFKY KLTIVGDGKY GARDADTKIW NGMVG ELVY GKADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSR FSP YEWHTEEFED GRETQSSEST NEFGIFNSLW FSLGAFMQQG CDISPRSLSG RIVGGVWWFF TLIIISSYTA NLAAFLT VE RMVSPIESAE DLSKQTEIAY GTLDSGSTKE FFRRSKIAVF DKMWTYMRSA EPSVFVRTTA EGVARVRKSK GKYAYLLE S TMNEYIEQRK PCDTMKVGGN LDSKGYGIAT PKGSSLGTPV NLAVLKLSEQ GVLDKLKNKW WYDKGECGAK DSGSKEKTS ALSLSNVAGV FYILVGGLGL AMLVALIEFC YKSRAEAKRM KGTGSACGRK ALTLLSSVFA VCGLGLLGIA VSTDYWLYLE EGIILPQNQ STEVKMSLHS GLWRVCFLAG EERGRCFTIE YVMPMNSQMT SESTVNVLKM IRSATPFPLV SLFFMFIGFI L SNIGHIRP HRTILAFVSG IFFILSGLSL VVGLVLYISS INDEMLNRTK DAETYFNYKY GWSFAFAAIS FLLTESAGVM SV YLFMKRY TA

UniProtKB: Glutamate receptor 2, Voltage-dependent calcium channel gamma-5 subunit

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Macromolecule #2: Protein cornichon homolog 1

MacromoleculeName: Protein cornichon homolog 1 / type: protein_or_peptide / ID: 2 / Details: human CNIH1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: kidney / Tissue: kidney
Molecular weightTheoretical: 16.707879 KDa
SequenceString:
MAFTFAAFCY MLALLLTAAL IFFAIWHIIA FDELKTDYKN PIDQCNTLNP LVLPEYLIHA FFCVMFLCAA EWLTLGLNMP LLAYHIWRY MSRPVMSGPG LYDPTTIMNA DILAYCQKEG WCKLAFYLLA FFYYLYGMIY VLVSS

UniProtKB: Protein cornichon homolog 1

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Macromolecule #3: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Macromolecule #4: N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide

MacromoleculeName: N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide
type: ligand / ID: 4 / Number of copies: 2 / Formula: FWF
Molecular weightTheoretical: 480.684 Da
Chemical component information

ChemComp-FWF:
N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris-HCl
1.0 mMC3H6SObeta mercaptoethanol
0.05 %C56H92O29digitonin
0.005 %C31H50O4cholesterol hemisuccinate
250.0 uMC14H14N2O2(R,R)-2b
5.0 mMC5H9NO4Glutamate

Details: 150 mM NaCl, 20 mM Tris-HCl pH 8.0, 1mM BME and 0.05% digitonin, 0.005% CHS, 250 uM (R,R)-2b, 5 mM glutamate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 500 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Detailsmonodisperse, multiview particles

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: 2712779
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: initial model from experimental data
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 209640
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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