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- PDB-11uf: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD) -

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Basic information

Entry
Database: PDB / ID: 11uf
TitleGluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD)
Components
  • Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
  • Protein cornichon homolog 1
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor (iGluR) / GluA2 / transmembrane AMPAR regulatory protein (TARP) / y5 / cornichon / CNIH1
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
Chem-FWF / GLUTAMIC ACID / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsGangwar, S.P. / Newton, T.P. / Yen, L.Y. / Sobolevsky, A.I.
Funding support United States, 7items
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, T.P. / Yelshanskaya, M.V. / Aktolun, M. / Gangwar, S.P. / Yen, L.Y. / Alekseev, A.A. / Sobolevsky, I.A. / Kurnikova, M.G. / Sobolevsky, A.I.
History
DepositionMar 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
B: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
C: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
D: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit
E: Protein cornichon homolog 1
F: Protein cornichon homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)504,92612
Polymers503,3766
Non-polymers1,5506
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-5 subunit / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / Neuronal voltage-gated calcium channel gamma-5 subunit / Transmembrane AMPAR regulatory protein gamma-5 / TARP gamma-5


Mass: 117489.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: rat GluA2 covalently fused to rat TARP y5,rat GluA2 covalently fused to rat TARP y5
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, GluA2, Glur2, Cacng5 / Plasmid: pEG BacMam / Cell (production host): epithelial / Cell line (production host): HEK 293S GnTI- / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney / References: UniProt: P19491, UniProt: Q8VHW4
#2: Protein Protein cornichon homolog 1 / CNIH-1 / Cornichon family AMPA receptor auxiliary protein 1 / Protein cornichon homolog / T-cell ...CNIH-1 / Cornichon family AMPA receptor auxiliary protein 1 / Protein cornichon homolog / T-cell growth-associated molecule 77 / TGAM77


Mass: 16707.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: human CNIH1 / Source: (natural) Homo sapiens (human) / Cell line: HEK 293S GnTI- / Organ: kidney / Tissue: kidney / References: UniProt: O95406
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FWF / N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide


Mass: 480.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H36N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GluA2-y5-CNIH1 open state + RR2b + Glu (LBD-TMD) / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK 293S GnTI- / Plasmid: pEG BacMam
Buffer solutionpH: 8
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
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTris-HClC4H11NO31
31 mMbeta mercaptoethanolC3H6SO1
40.05 %digitoninC56H92O291
50.005 %cholesterol hemisuccinateC31H50O41
6250 uM(R,R)-2bC14H14N2O21
75 mMGlutamateC5H9NO41
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: monodisperse, multiview particles
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.11.1_2575model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2712779
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209640 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00718744
ELECTRON MICROSCOPYf_angle_d1.10625348
ELECTRON MICROSCOPYf_dihedral_angle_d11.2311026
ELECTRON MICROSCOPYf_chiral_restr0.0552836
ELECTRON MICROSCOPYf_plane_restr0.0093116

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