+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43276 | ||||||||||||||||||
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Title | GluA2 bound to GYKI-52466 and Glutamate, Inhibited State 2 | ||||||||||||||||||
Map data | Inhibited state 2 full map | ||||||||||||||||||
Sample |
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Keywords | ligand gated ion channel / ionotropic glutamate receptor / allosteric inhibition / MEMBRANE PROTEIN / MEMBRANE PROTEIN-INHIBITOR complex | ||||||||||||||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.85 Å | ||||||||||||||||||
Authors | Hale WD / Montano Romero A / Huganir RL / Twomey EC | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Allosteric competition and inhibition in AMPA receptors. Authors: W Dylan Hale / Alejandra Montaño Romero / Cuauhtemoc U Gonzalez / Vasanthi Jayaraman / Albert Y Lau / Richard L Huganir / Edward C Twomey / Abstract: Excitatory neurotransmission is principally mediated by α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-subtype ionotropic glutamate receptors (AMPARs). Negative allosteric modulators ...Excitatory neurotransmission is principally mediated by α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-subtype ionotropic glutamate receptors (AMPARs). Negative allosteric modulators are therapeutic candidates that inhibit AMPAR activation and can compete with positive modulators to control AMPAR function through unresolved mechanisms. Here we show that allosteric inhibition pushes AMPARs into a distinct state that prevents both activation and positive allosteric modulation. We used cryo-electron microscopy to capture AMPARs bound to glutamate, while a negative allosteric modulator, GYKI-52466, and positive allosteric modulator, cyclothiazide, compete for control of the AMPARs. GYKI-52466 binds in the ion channel collar and inhibits AMPARs by decoupling the ligand-binding domains from the ion channel. The rearrangement of the ligand-binding domains ruptures the cyclothiazide site, preventing positive modulation. Our data provide a framework for understanding allostery of AMPARs and for rational design of therapeutics targeting AMPARs in neurological diseases. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43276.map.gz | 12.1 MB | EMDB map data format | |
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Header (meta data) | emd-43276-v30.xml emd-43276.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
Images | emd_43276.png | 23.4 KB | ||
Filedesc metadata | emd-43276.cif.gz | 6.3 KB | ||
Others | emd_43276_additional_1.map.gz emd_43276_additional_2.map.gz emd_43276_half_map_1.map.gz emd_43276_half_map_2.map.gz | 4.2 MB 2.7 MB 205.1 MB 205 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43276 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43276 | HTTPS FTP |
-Validation report
Summary document | emd_43276_validation.pdf.gz | 974.8 KB | Display | EMDB validaton report |
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Full document | emd_43276_full_validation.pdf.gz | 974.4 KB | Display | |
Data in XML | emd_43276_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_43276_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43276 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43276 | HTTPS FTP |
-Related structure data
Related structure data | 8vj7MC 8vj6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43276.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Inhibited state 2 full map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: LBD TMD local map
File | emd_43276_additional_1.map | ||||||||||||
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Annotation | LBD TMD local map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TMD local map
File | emd_43276_additional_2.map | ||||||||||||
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Annotation | TMD local map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Inhibited state 2 full half B
File | emd_43276_half_map_1.map | ||||||||||||
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Annotation | Inhibited state 2 full half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Inhibited state 2 full half A
File | emd_43276_half_map_2.map | ||||||||||||
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Annotation | Inhibited state 2 full half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AMPA Receptor GluA2 Homotetramer
Entire | Name: AMPA Receptor GluA2 Homotetramer |
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Components |
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-Supramolecule #1: AMPA Receptor GluA2 Homotetramer
Supramolecule | Name: AMPA Receptor GluA2 Homotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Macromolecule #1: Isoform Flip of Glutamate receptor 2
Macromolecule | Name: Isoform Flip of Glutamate receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 89.232961 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NSIQIGGLFP RGADQEYSAF RVGMVQFSTS EFRLTPHIDN LEVANSFAVT NAFCSQFSRG VYAIFGFYDK KSVNTITSFC GTLHVSFIT PSFPTDGTHP FVIQMRPDLK GALLSLIEYY QWDKFAYLYD SDRGLSTLQA VLDSAAEKKW QVTAINVGNI N NDKKDETY ...String: NSIQIGGLFP RGADQEYSAF RVGMVQFSTS EFRLTPHIDN LEVANSFAVT NAFCSQFSRG VYAIFGFYDK KSVNTITSFC GTLHVSFIT PSFPTDGTHP FVIQMRPDLK GALLSLIEYY QWDKFAYLYD SDRGLSTLQA VLDSAAEKKW QVTAINVGNI N NDKKDETY RSLFQDLELK KERRVILDCE RDKVNDIVDQ VITIGKHVKG YHYIIANLGF TDGDLLKIQF GGAEVSGFQI VD YDDSLVS KFIERWSTLE EKEYPGAHTA TIKYTSALTY DAVQVMTEAF RNLRKQRIEI SRRGNAGDCL ANPAVPWGQG VEI ERALKQ VQVEGLSGNI KFDQNGKRIN YTINIMELKT NGPRKIGYWS EVDKMVLTED DTSGLEQKTV VVTTILESPY VMMK KNHEM LEGNERYEGY CVDLAAEIAK HCGFKYKLTI VGDGKYGARD ADTKIWNGMV GELVYGKADI AIAPLTITLV REEVI DFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVVLFLV SRFSPYSEST NEFGIFNSLW FSLGAF MQQ GCDISPRSLS GRIVGGVWWF FTLIIISSYT ANLAAFLTVE RMVSPIESAE DLSKQTEIAY GTLDSGSTKE FFRRSKI AV FDKMWTYMRS AEPSVFVRTT AEGVARVRKS KGKYAYLLES TMNEYIEQRK PCDTMKVGGN LDSKGYGIAT PKGSSLGT P VNLAVLKLSE QGVLDKLKNK WWYDKGECGA KDSGSKEKTS ALSLSNVAGV FYILVGGLGL AMLVALIEFC YKSRAE UniProtKB: Glutamate receptor 2 |
-Macromolecule #2: GLUTAMIC ACID
Macromolecule | Name: GLUTAMIC ACID / type: ligand / ID: 2 / Number of copies: 4 / Formula: GLU |
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Molecular weight | Theoretical: 147.129 Da |
Chemical component information | ChemComp-GLU: |
-Macromolecule #3: 4-[(5S,8R)-8-methyl-6,7,8,9-tetrahydro-2H,5H-[1,3]dioxolo[4,5-h][...
Macromolecule | Name: 4-[(5S,8R)-8-methyl-6,7,8,9-tetrahydro-2H,5H-[1,3]dioxolo[4,5-h][2,3]benzodiazepin-5-yl]aniline type: ligand / ID: 3 / Number of copies: 4 / Formula: A1AB5 |
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Molecular weight | Theoretical: 293.32 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ab initio |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 130474 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |