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Yorodumi- EMDB-44244: GluA2 flip Q in complex with TARPgamma2 at pH5, consensus structu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44244 | |||||||||||||||
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Title | GluA2 flip Q in complex with TARPgamma2 at pH5, consensus structure of TMD-TARPgamma2 | |||||||||||||||
Map data | GluA2 flip Q isoform in complex with TARPgamma2 at pH5.3, consensus map of TMD-TARPgamma2 | |||||||||||||||
Sample |
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Keywords | AMPA receptor / ionotropic glutamate receptor / ion channel / auxiliary subunit / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | Function and homology information Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / regulation of postsynaptic neurotransmitter receptor activity / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / regulation of AMPA receptor activity / neurotransmitter receptor internalization ...Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / regulation of postsynaptic neurotransmitter receptor activity / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / regulation of AMPA receptor activity / neurotransmitter receptor internalization / membrane hyperpolarization / postsynaptic neurotransmitter receptor diffusion trapping / nervous system process / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / channel regulator activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / regulation of postsynaptic membrane neurotransmitter receptor levels / immunoglobulin binding / membrane depolarization / 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 / voltage-gated calcium channel activity / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / positive regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / 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 binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / postsynaptic density membrane / response to calcium ion / modulation of chemical synaptic transmission / establishment of protein localization / 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 / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) / Rattus norvegicus (Norway rat) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||||||||
Authors | Nakagawa T / Greger IH | |||||||||||||||
Funding support | United States, United Kingdom, 4 items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: Proton-triggered rearrangement of the AMPA receptor N-terminal domains impacts receptor kinetics and synaptic localization Authors: Ivica J / Kejzar N / Ho H / Stockwell I / Kuchtiak V / Scrutton AM / Nakagawa T / Greger IH | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44244.map.gz | 166.6 MB | EMDB map data format | |
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Header (meta data) | emd-44244-v30.xml emd-44244.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44244_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_44244.png | 118.3 KB | ||
Filedesc metadata | emd-44244.cif.gz | 7 KB | ||
Others | emd_44244_half_map_1.map.gz emd_44244_half_map_2.map.gz | 140.8 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44244 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44244 | HTTPS FTP |
-Related structure data
Related structure data | 9b63MC 9b5zC 9b60C 9b61C 9b64C 9b67C 9b68C 9b69C 9b6aC C: citing same article (ref.) M: atomic model generated by this map |
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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_44244.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | GluA2 flip Q isoform in complex with TARPgamma2 at pH5.3, consensus map of TMD-TARPgamma2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half1 map: GluA2 flip Q isoform in complex...
File | emd_44244_half_map_1.map | ||||||||||||
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Annotation | Half1 map: GluA2 flip Q isoform in complex with TARPgamma2 at pH5.3, consensus map of TMD-TARPgamma2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map: GluA2 flip Q isoform in complex...
File | emd_44244_half_map_2.map | ||||||||||||
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Annotation | Half2 map: GluA2 flip Q isoform in complex with TARPgamma2 at pH5.3, consensus map of TMD-TARPgamma2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GluA2 (flip-Q isoform) in complex with TARPgamma2 at 4:4 stoichiometry
Entire | Name: GluA2 (flip-Q isoform) in complex with TARPgamma2 at 4:4 stoichiometry |
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Components |
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-Supramolecule #1: GluA2 (flip-Q isoform) in complex with TARPgamma2 at 4:4 stoichiometry
Supramolecule | Name: GluA2 (flip-Q isoform) in complex with TARPgamma2 at 4:4 stoichiometry type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Voltage-dependent calcium channel gamma-2 subunit
Macromolecule | Name: Voltage-dependent calcium channel gamma-2 subunit / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 35.938746 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD ...String: MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD SKKNSYSYGW SFYFGALSFI IAEMVGVLAV HMFIDRHKQL RATARATDYL QASAITRIPS YRYRYQRRSR SS SRSTEPS HSRDASPVGV KGFNTLPSTE ISMYTLSRDP LKAATTPTAT YNSDRDNSFL QVHNCIQKDS KDSLHANTAN RRT TPV UniProtKB: Voltage-dependent calcium channel gamma-2 subunit |
-Macromolecule #2: Isoform Flip of Glutamate receptor 2
Macromolecule | Name: Isoform Flip of Glutamate receptor 2 / type: protein_or_peptide / ID: 2 / Details: A FLAG epitope tag is inserted near the C-terminus / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 99.617492 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 LKIQFGGANV SGFQIVDYDD SLVSKFIERW STLEEKEYPG AHTATIKYTS ALTYDAVQVM TEAFRNLRKQ RIE ISRRGN AGDCLANPAV PWGQGVEIER ALKQVQVEGL SGNIKFDQNG KRINYTINIM ELKTNGPRKI GYWSEVDKMV VTLT ELPSG NDTSGLENKT VVVTTILESP YVMMKKNHEM LEGNERYEGY CVDLAAEIAK HCGFKYKLTI VGDGKYGARD ADTKI WNGM VGELVYGKAD IAIAPLTITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVV LFL VSRFSPYEWH TEEFEDGRET QSSESTNEFG IFNSLWFSLG AFMQQGCDIS PRSLSGRIVG GVWWFFTLII ISSYTAN LA AFLTVERMVS PIESAEDLSK QTEIAYGTLD SGSTKEFFRR SKIAVFDKMW TYMRSAEPSV FVRTTAEGVA RVRKSKGK Y AYLLESTMNE YIEQRKPCDT MKVGGNLDSK GYDIATPKGS SLGTPVNLAV LKLSEQGVLD KLKNKWWYDK GECGAKDSG SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NPQNINPSSS QNSQNFATDY KDDDDKEGYN VYGIESVKI UniProtKB: Glutamate receptor 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
Details: Tris adjusted to pH 8 using HCl. 4 micro litter of protein in buffer was mixed with 1 micro litter of 50mM citric acid buffer (the 50mM citric acid buffer was prepared by diluting 0.5M ...Details: Tris adjusted to pH 8 using HCl. 4 micro litter of protein in buffer was mixed with 1 micro litter of 50mM citric acid buffer (the 50mM citric acid buffer was prepared by diluting 0.5M citric acid/sodium citrate buffer at pH4.0) immediately before applying the sample to the grid. | ||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 19684 / Average electron dose: 55.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |