+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16379 | |||||||||
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タイトル | Active state homomeric GluA1 AMPA receptor in complex with TARP gamma 3 | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | AMPAR / ion channels / neurotransmission / MEMBRANE PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / cellular response to ammonium ion / proximal dendrite / neurotransmitter receptor transport, postsynaptic endosome to lysosome ...Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / cellular response to ammonium ion / proximal dendrite / neurotransmitter receptor transport, postsynaptic endosome to lysosome / response to sucrose / LGI-ADAM interactions / myosin V binding / Trafficking of AMPA receptors / neuron spine / cellular response to dsRNA / cellular response to L-glutamate / regulation of AMPA receptor activity / conditioned place preference / neurotransmitter receptor internalization / response to arsenic-containing substance / postsynaptic neurotransmitter receptor diffusion trapping / regulation of monoatomic ion transmembrane transport / dendritic spine membrane / Synaptic adhesion-like molecules / long-term synaptic depression / response to morphine / cellular response to peptide hormone stimulus / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / protein kinase A binding / peptide hormone receptor binding / response to psychosocial stress / spinal cord development / neuronal cell body membrane / Activation of AMPA receptors / behavioral response to pain / perisynaptic space / AMPA glutamate receptor activity / transmission of nerve impulse / channel regulator activity / cellular response to organic cyclic compound / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / excitatory synapse / adenylate cyclase binding / positive regulation of excitatory postsynaptic potential / ionotropic glutamate receptor complex / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / asymmetric synapse / neuronal action potential / regulation of receptor recycling / G-protein alpha-subunit binding / Unblocking of NMDA receptors, glutamate binding and activation / voltage-gated calcium channel activity / glutamate receptor binding / protein targeting / positive regulation of synaptic transmission / response to electrical stimulus / long-term memory / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / dendritic shaft / response to cocaine / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / cellular response to amino acid stimulus / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / neuromuscular junction / response to organic cyclic compound / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / cellular response to growth factor stimulus / receptor internalization / recycling endosome / cerebral cortex development / response to peptide hormone / small GTPase binding / response to toxic substance / synaptic vesicle membrane / recycling endosome membrane / G-protein beta-subunit binding / cell-cell junction 類似検索 - 分子機能 | |||||||||
生物種 | Rattus (ネズミ) / Rattus norvegicus (ドブネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.9 Å | |||||||||
データ登録者 | Zhang D / Ivica J / Krieger JM / Ho H / Yamashita K / Cais O / Greger I | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Nature / 年: 2023 タイトル: Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor. 著者: Danyang Zhang / Josip Ivica / James M Krieger / Hinze Ho / Keitaro Yamashita / Imogen Stockwell / Rozbeh Baradaran / Ondrej Cais / Ingo H Greger / 要旨: AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. ...AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. Despite their prominent expression throughout interneurons and glia, their role in long-term potentiation and their involvement in a range of neuropathologies, structural information for GluA2-lacking receptors is currently absent. Here we determine and characterize cryo-electron microscopy structures of the GluA1 homotetramer, fully occupied with TARPγ3 auxiliary subunits (GluA1/γ3). The gating core of both resting and open-state GluA1/γ3 closely resembles GluA2-containing receptors. However, the sequence-diverse N-terminal domains (NTDs) give rise to a highly mobile assembly, enabling domain swapping and subunit re-alignments in the ligand-binding domain tier that are pronounced in desensitized states. These transitions underlie the unique kinetic properties of GluA1. A GluA2 mutant (F231A) increasing NTD dynamics phenocopies this behaviour, and exhibits reduced synaptic responses, reflecting the anchoring function of the AMPAR NTD at the synapse. Together, this work underscores how the subunit-diverse NTDs determine subunit arrangement, gating properties and ultimately synaptic signalling efficiency among AMPAR subtypes. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_16379.map.gz | 15.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16379-v30.xml emd-16379.xml | 18.2 KB 18.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16379_fsc.xml | 14.7 KB | 表示 | FSCデータファイル |
画像 | emd_16379.png | 86.2 KB | ||
マスクデータ | emd_16379_msk_1.map | 93 MB | マスクマップ | |
Filedesc metadata | emd-16379.cif.gz | 6.8 KB | ||
その他 | emd_16379_half_map_1.map.gz emd_16379_half_map_2.map.gz | 85.8 MB 85.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16379 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16379 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16379_validation.pdf.gz | 942.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_16379_full_validation.pdf.gz | 942.2 KB | 表示 | |
XML形式データ | emd_16379_validation.xml.gz | 19.7 KB | 表示 | |
CIF形式データ | emd_16379_validation.cif.gz | 26.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16379 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16379 | HTTPS FTP |
-関連構造データ
関連構造データ | 8c1pMC 8c1qC 8c1rC 8c1sC 8c2hC 8c2iC 8p3qC 8p3sC 8p3tC 8p3uC 8p3vC 8p3wC 8p3xC 8p3yC 8p3zC 8pivC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_16379.map.gz / 形式: CCP4 / 大きさ: 93 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.826 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_16379_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_16379_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_16379_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Homomeric GluA1 AMPA receptor in complex with TARP gamma 3
全体 | 名称: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3 |
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要素 |
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-超分子 #1: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3
超分子 | 名称: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #2 |
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由来(天然) | 生物種: Rattus (ネズミ) |
-分子 #1: Glutamate receptor 1 flip isoform
分子 | 名称: Glutamate receptor 1 flip isoform / タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 102.66193 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR ...文字列: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR VLDTAAEKNW QVTAVNILTT TEEGYRMLFQ DLEKKKERLV VVDCESERLN AILGQIVKLE KNGIGYHYIL AN LGFMDID LNKFKESGAN VTGFQLVNYT DTIPARIMQQ WRTSDSRDHT RVDWKRPKYT SALTYDGVKV MAEAFQSLRR QRI DISRRG NAGDCLANPA VPWGQGIDIQ RALQQVRFEG LTGNVQFNEK GRRTNYTLHV IEMKHDGIRK IGYWNEDDKF VPAA TDAQA GGDNSSVQNR TYIVTTILED PYVMLKKNAN QFEGNDRYEG YCVELAAEIA KHVGYSYRLE IVSDGKYGAR DPDTK AWNG MVGELVYGRA DVAVAPLTIT LVREEVIDFS KPFMSLGISI MIKKPQKSKP GVFSFLDPLA YEIWMCIVFA YIGVSV VLF LVSRFSPYEW HSEEFEEGRD QTTSDQSNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTA NL AAFLTVERMV SPIESAEDLA KQTEIAYGTL EAGSTKEFFR RSKIAVFEKM WTYMKSAEPS VFVRTTEEGM IRVRKSKG K YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SALRGPVNLA VLKLSEQGVL DKLKSKWWYD KGECGSKDS GSKDKTSALS LSNVAGVFYI LIGGLGLAML VALIEFCYKS RSESKRMKGF CLIPQQSINE AIRTSTLPRN SGAGASGGGG SGENGRVVS QDFPKSMQSI PCMSHSSGMP LGATGL UniProtKB: Glutamate receptor 1 |
-分子 #2: Voltage-dependent calcium channel gamma-3 subunit
分子 | 名称: Voltage-dependent calcium channel gamma-3 subunit / タイプ: protein_or_peptide / ID: 2 / コピー数: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 35.435332 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: RMCDRGIQML ITTVGAFAAF SLMTIAVGTD YWLYSRGVCR TKSTSDNETS RKNEEVMTHS GLWRTCCLEG AFRGVCKKID HFPEDADYE QDTAEYLLRA VRASSVFPIL SVTLLFFGGL CVAASEFHRS RHSVILSAGI FFVSAGLSNI IGIIVYISAN A GDPGQRDS ...文字列: RMCDRGIQML ITTVGAFAAF SLMTIAVGTD YWLYSRGVCR TKSTSDNETS RKNEEVMTHS GLWRTCCLEG AFRGVCKKID HFPEDADYE QDTAEYLLRA VRASSVFPIL SVTLLFFGGL CVAASEFHRS RHSVILSAGI FFVSAGLSNI IGIIVYISAN A GDPGQRDS KKSYSYGWSF YFGAFSFIIA EIVGVVAVHI YIEKHQQLRA RSHSELLKKS TFARLPPYRY RFRRRSSSRS TE PRSRDLS PISKGFHTIP STDISMFTLS RDPSKLTMGT LLNSDRDHAF LQFHNSTPKE FKESLHNNPA NRRTTPV UniProtKB: Voltage-dependent calcium channel gamma-3 subunit |
-分子 #3: CYCLOTHIAZIDE
分子 | 名称: CYCLOTHIAZIDE / タイプ: ligand / ID: 3 / コピー数: 4 / 式: CYZ |
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分子量 | 理論値: 389.878 Da |
Chemical component information |
-分子 #4: PALMITIC ACID
分子 | 名称: PALMITIC ACID / タイプ: ligand / ID: 4 / コピー数: 6 / 式: PLM |
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分子量 | 理論値: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-分子 #5: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
分子 | 名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / タイプ: ligand / ID: 5 / コピー数: 4 / 式: OLC |
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分子量 | 理論値: 356.54 Da |
Chemical component information | ChemComp-OLC: |
-分子 #6: GLUTAMIC ACID
分子 | 名称: GLUTAMIC ACID / タイプ: ligand / ID: 6 / コピー数: 4 / 式: GLU |
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分子量 | 理論値: 147.129 Da |
Chemical component information | ChemComp-GLU: |
-分子 #7: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
分子 | 名称: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate タイプ: ligand / ID: 7 / コピー数: 2 / 式: POV |
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分子量 | 理論値: 760.076 Da |
Chemical component information | ChemComp-POV: |
-分子 #8: water
分子 | 名称: water / タイプ: ligand / ID: 8 / コピー数: 64 / 式: HOH |
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分子量 | 理論値: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 8 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.4 µm 最小 デフォーカス(公称値): 1.4000000000000001 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
詳細 | Servalcat |
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精密化 | 空間: RECIPROCAL |
得られたモデル | PDB-8c1p: |