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- PDB-9e9e: Structure of AMPA receptor GluA2 and auxiliary subunit TARP gamma... -

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Basic information

Entry
Database: PDB / ID: 9e9e
TitleStructure of AMPA receptor GluA2 and auxiliary subunit TARP gamma-2 (LBD-TMD) in complex with anti-miR 17 oligonucleotide RGLS4326
ComponentsIsoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
KeywordsSIGNALING PROTEIN / AMPA receptor / TARP gamma-2 / ion channel / anti-miR 17 / oligonucleotide
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / postsynaptic neurotransmitter receptor diffusion trapping / channel regulator activity / LGI-ADAM interactions / Trafficking of AMPA receptors / regulation of AMPA receptor activity / membrane hyperpolarization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / postsynaptic neurotransmitter receptor diffusion trapping / channel regulator activity / LGI-ADAM interactions / Trafficking of AMPA receptors / regulation of AMPA receptor activity / membrane hyperpolarization / nervous system process / protein targeting to membrane / voltage-gated calcium channel complex / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / neurotransmitter receptor localization to postsynaptic specialization membrane / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / neuromuscular junction development / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / transmission of nerve impulse / AMPA glutamate receptor clustering / kainate selective glutamate receptor activity / cellular response to glycine / AMPA glutamate receptor complex / immunoglobulin binding / asymmetric synapse / extracellularly glutamate-gated ion channel activity / regulation of receptor recycling / ionotropic glutamate receptor complex / membrane depolarization / conditioned place preference / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / positive regulation of synaptic transmission, glutamatergic / regulation of synaptic transmission, glutamatergic / regulation of postsynaptic membrane neurotransmitter receptor levels / response to fungicide / voltage-gated calcium channel activity / glutamate-gated receptor activity / cytoskeletal protein binding / extracellular ligand-gated monoatomic ion channel activity / regulation of long-term synaptic depression / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / excitatory synapse / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / dendritic shaft / SNARE binding / PDZ domain binding / calcium channel regulator activity / synaptic transmission, glutamatergic / regulation of membrane potential / protein tetramerization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of protein localization / response to calcium ion / cerebral cortex development / postsynaptic density membrane / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / synaptic vesicle membrane / signaling receptor activity / amyloid-beta binding / presynapse / growth cone / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding
Similarity search - Function
Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family / 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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel ...Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family / 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 / 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 2 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsYen, L.Y. / Gangwar, S.P. / Yelshanskaya, M.V. / Sobolevsky, A.I.
Funding support United States, 2items
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
CitationJournal: Nat Commun / Year: 2025
Title: The nucleobase guanine at the 3'-terminus of oligonucleotide RGLS4326 drives off-target AMPAR inhibition and CNS toxicity.
Authors: Tania Valencia / Laura Y Yen / Cindy Berman / Thomas Vincent / Scott Davis / Francesca Varrone / Jianfeng Huang / Jessica Mastroianni / Morgan Carlson / Tate Owen / Amin Kamel / Denis Drygin ...Authors: Tania Valencia / Laura Y Yen / Cindy Berman / Thomas Vincent / Scott Davis / Francesca Varrone / Jianfeng Huang / Jessica Mastroianni / Morgan Carlson / Tate Owen / Amin Kamel / Denis Drygin / Garth A Kinberger / Shanti Pal Gangwar / Maria V Yelshanskaya / John Ridley / Robert Kirby / Jesus Alvarez / Ronak Lakhia / Vishal Patel / Alexander I Sobolevsky / Edmund C Lee /
Abstract: Designing safe and effective oligonucleotide (ON) therapeutics requires thorough understanding of structural-activity relationship (SAR) with the intended on-target(s) as well as the unintended off- ...Designing safe and effective oligonucleotide (ON) therapeutics requires thorough understanding of structural-activity relationship (SAR) with the intended on-target(s) as well as the unintended off-target(s). Despite encouraging pharmacodynamic activity in a Phase 1b study, development of the first-generation anti-miR-17 ON RGLS4326 for the treatment of autosomal dominant polycystic kidney disease was discontinued due to dose-limiting central nervous system (CNS)-related toxicity observed in nonclinical chronic toxicity studies. Here, we provide SAR evidence that the nucleobase guanine at the 3'-terminus of RGLS4326 drives an unexpected off-target aptamer-like direct interaction with α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR), thereby causing CNS toxicity. By replacing the 3'-terminal guanine with adenine, we discover the next-generation anti-miR-17 RGLS8429 that is devoid of off-target AMPAR interaction and CNS toxicity while preserving the potency against the on-target miR-17. Here, we show a way to avoid off-target CNS effects and, more importantly, data that support the clinical development of RGLS8429.
History
DepositionNov 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
B: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
C: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
D: Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)463,5968
Polymers459,6854
Non-polymers3,9114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
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-2 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-2 subunit / Stargazin / Transmembrane AMPAR regulatory protein gamma-2 / TARP gamma-2


Mass: 114921.297 Da / Num. of mol.: 4 / Mutation: N48D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, GluA2, Glur2, Cacng2, Stg / Plasmid: pEG BacMam / Cell line (production host): HEK293S-GnTi / Production host: Homo sapiens (human) / References: UniProt: P19491, UniProt: Q71RJ2
#2: Chemical
ChemComp-A1BX3 / O-{[(1S,3S,4R,6S,7R)-7-{[(R)-{[(1R,3R,4R,6S,7R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-7-hydroxy-6-methyl-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy}(sulfanyl)phosphoryl]oxy}-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-methyl-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methyl} O-[(2R,3S,4R,5S)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-methoxy-2-methyloxolan-3-yl] hydrogen (R)-phosphorothioate


Mass: 977.806 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H41N9O18P2S2 / 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-y2 + oligo RGLS 4326 / Type: COMPLEX
Details: LBD-TMD of AMPA receptor GluA2 in complex with auxiliary subunit TARP gamma-2 bound to anti-miR 17 oligonucleotide RGLS 4326
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S-GnTi / Plasmid: pEG BacMam
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtrisC4H11NO31
2150 mMsodium chlorideNaCl1
30.05 %digitoninC56H92O291
SpecimenConc.: 3.24 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Protein extracted and purified in detergent micelle
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 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
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192000 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00519154
ELECTRON MICROSCOPYf_angle_d0.69926086
ELECTRON MICROSCOPYf_dihedral_angle_d10.88311150
ELECTRON MICROSCOPYf_chiral_restr0.0432902
ELECTRON MICROSCOPYf_plane_restr0.0043114

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