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Yorodumi- EMDB-20717: GluA2 in complex with complex full-length in AS, bound to antagon... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20717 | |||||||||
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Title | GluA2 in complex with complex full-length in AS, bound to antagonist ZK200775 | |||||||||
Map data | GluA2/CNIH3 complex full-length in AS, bound to antagonist ZK200775 | |||||||||
Sample |
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Function / homology | Function and homology information Cargo concentration in the ER / COPII-mediated vesicle transport / localization within membrane / regulation of AMPA receptor activity / channel regulator activity / neurotransmitter receptor localization to postsynaptic specialization membrane / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors ...Cargo concentration in the ER / COPII-mediated vesicle transport / localization within membrane / regulation of AMPA receptor activity / channel regulator activity / neurotransmitter receptor localization to postsynaptic specialization membrane / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / COPII-coated ER to Golgi transport vesicle / 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 / endoplasmic reticulum to Golgi vesicle-mediated transport / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / 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 / regulation of membrane potential / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Nakagawa T | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2019 Title: Structures of the AMPA receptor in complex with its auxiliary subunit cornichon. Authors: Terunaga Nakagawa / Abstract: In the brain, AMPA-type glutamate receptors (AMPARs) form complexes with their auxiliary subunits and mediate the majority of fast excitatory neurotransmission. Signals transduced by these complexes ...In the brain, AMPA-type glutamate receptors (AMPARs) form complexes with their auxiliary subunits and mediate the majority of fast excitatory neurotransmission. Signals transduced by these complexes are critical for synaptic plasticity, learning, and memory. The two major categories of AMPAR auxiliary subunits are transmembrane AMPAR regulatory proteins (TARPs) and cornichon homologs (CNIHs); these subunits share little homology and play distinct roles in controlling ion channel gating and trafficking of AMPAR. Here, I report high-resolution cryo-electron microscopy structures of AMPAR in complex with CNIH3. Contrary to its predicted membrane topology, CNIH3 lacks an extracellular domain and instead contains four membrane-spanning helices. The protein-protein interaction interface that dictates channel modulation and the lipids surrounding the complex are revealed. These structures provide insights into the molecular mechanism for ion channel modulation and assembly of AMPAR/CNIH3 complexes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20717.map.gz | 20.7 MB | EMDB map data format | |
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Header (meta data) | emd-20717-v30.xml emd-20717.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20717_fsc.xml | 6.4 KB | Display | FSC data file |
Images | emd_20717.png | 203.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20717 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20717 | HTTPS FTP |
-Validation report
Summary document | emd_20717_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_20717_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_20717_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20717 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20717 | HTTPS FTP |
-Related structure data
Related structure data | 6peqC 6u5sC 6u6iC 6ucbC 6ud4C 6ud8C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20717.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | GluA2/CNIH3 complex full-length in AS, bound to antagonist ZK200775 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.132 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GluA2 in complex with CNIH3 full length at 4:4 stoichiometry
Entire | Name: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry |
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Components |
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-Supramolecule #1: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry
Supramolecule | Name: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Bound to antagonist ZK200775 (MPQX). Lipid densities are observed. |
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Molecular weight | Theoretical: 470 KDa |
-Supramolecule #2: Glutamate receptor 2
Supramolecule | Name: Glutamate receptor 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK |
-Supramolecule #3: Protein cornichon homolog 3
Supramolecule | Name: Protein cornichon homolog 3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK |
-Macromolecule #1: Glutamate receptor 2
Macromolecule | Name: Glutamate receptor 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIFG FYDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE ...String: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIFG FYDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE KKWQVTAINV GNINNDKKDE TYRSLFQDLE LKKERRVILD CERDKVNDIV DQVITIGKHV KGYHYIIANL GFTDGDLLKI QFGGANVSGF QIVDYDDSLV SKFIERWSTL EEKEYPGAHT ATIKYTSALT YDAVQVMTEA FRNLRKQRIE ISRRGNAGDC LANPAVPWGQ GVEIERALKQ VQVEGLSGNI KFDQNGKRIN YTINIMELKT NGPRKIGYWS EVDKMVVTLT ELPSGNDTSG LENKTVVVTT ILESPYVMMK KNHEMLEGNE RYEGYCVDLA AEIAKHCGFK YKLTIVGDGK YGARDADTKI WNGMVGELVY GKADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSRFSPY EWHTEEFEDG RETQSSESTN EFGIFNSLWF SLGAFMRQGC DISPRSLSGR IVGGVWWFFT LIIISSYTAN LAAFLTVERM VSPIESAEDL SKQTEIAYGT LDSGSTKEFF RRSKIAVFDK MWTYMRSAEP SVFVRTTAEG VARVRKSKGK YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SSLGNAVNLA VLKLNEQGLL DKLKNKWWYD KGECGSGGGD SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NPQNINPSSS QNSQNFATDY KDDDDKEGYN VYGIESVKI |
-Macromolecule #2: Protein cornichon homolog 3
Macromolecule | Name: Protein cornichon homolog 3 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAFTFAAFCY MLSLVLCAAL IFFAIWHIIA FDELRTDFKS PIDQCNPVHA RERLRNIERI CFLLRKLVLP EYSIHSLFCI MFLCAQEWLT LGLNVPLLFY HFWRYFHCPA DSSELAYDPP VVMNADTLSY CQKEAWCKLA FYLLSFFYYL YCMIYTLVSS GGRGGTETSQ VAPA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11340 / Average exposure time: 6.0 sec. / Average electron dose: 58.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
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
-Atomic model buiding 1
Refinement | Space: REAL |
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