+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8c1q | |||||||||
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タイトル | Resting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3 | |||||||||
要素 |
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キーワード | MEMBRANE PROTEIN / AMPAR / ion channels / neurotransmission | |||||||||
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 norvegicus (ドブネズミ) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.82 Å | |||||||||
データ登録者 | Zhang, D. / Ivica, J. / Krieger, J.M. / 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
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8c1q.cif.gz | 514.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8c1q.ent.gz | 391.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8c1q.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8c1q_validation.pdf.gz | 1.8 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8c1q_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 8c1q_validation.xml.gz | 80.2 KB | 表示 | |
CIF形式データ | 8c1q_validation.cif.gz | 116.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/c1/8c1q ftp://data.pdbj.org/pub/pdb/validation_reports/c1/8c1q | HTTPS FTP |
-関連構造データ
関連構造データ | 16380MC 8c1pC 8c1rC 8c1sC 8c2hC 8c2iC 8p3qC 8p3sC 8p3tC 8p3uC 8p3vC 8p3wC 8p3xC 8p3yC 8p3zC 8pivC M: このデータのモデリングに利用したマップデータ 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
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 2種, 8分子 ABCDEFGH
#1: タンパク質 | 分子量: 102661.930 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Gria1, Glur1 / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P19490 #2: タンパク質 | 分子量: 35435.332 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Cacng3 / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8VHX0 |
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-非ポリマー , 5種, 43分子
#3: 化合物 | ChemComp-ZK1 / {[ #4: 化合物 | ChemComp-PLM / #5: 化合物 | ChemComp-OLC / ( #6: 化合物 | ChemComp-POV / ( #7: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3 タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT |
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由来(天然) | 生物種: Rattus (ネズミ) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: TFS KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2400 nm / 最小 デフォーカス(公称値): 1400 nm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
EMソフトウェア | 名称: REFMAC / カテゴリ: モデル精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.82 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 252544 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 空間: RECIPROCAL / 詳細: Servalcat | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | 解像度: 2.82→2.82 Å / Cor.coef. Fo:Fc: 0.922 / SU B: 9.356 / SU ML: 0.174 / ESU R: 0.292 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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溶媒の処理 | 溶媒モデル: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 135.112 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: 1 / 合計: 18462 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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