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基本情報
登録情報 | データベース: PDB / ID: 8g5g | |||||||||
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タイトル | Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA, Zolpidem, and endogenous neurosteroid | |||||||||
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![]() | MEMBRANE PROTEIN / ligand-gated ion channel / cys-loop receptor / neurotransmitter receptor | |||||||||
機能・相同性 | ![]() GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / diazepam binding / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / cellular response to histamine / inner ear receptor cell development / GABA-A receptor activity / GABA-gated chloride ion channel activity ...GABA receptor activation / inhibitory extracellular ligand-gated monoatomic ion channel activity / diazepam binding / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / cellular response to histamine / inner ear receptor cell development / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / innervation / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / neurotransmitter receptor activity / adult behavior / cochlea development / chloride channel activity / chloride channel complex / transmembrane transporter complex / GABA-ergic synapse / neuron development / regulation of postsynaptic membrane potential / presynaptic active zone membrane / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / cytoplasmic vesicle / chemical synaptic transmission / postsynapse / neuron projection / axon / glutamatergic synapse / synapse / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
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: 2.94 Å | |||||||||
![]() | Sun, C. / Gouaux, E. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM structures reveal native GABA receptor assemblies and pharmacology. 著者: Chang Sun / Hongtao Zhu / Sarah Clark / Eric Gouaux / ![]() ![]() 要旨: Type A γ-aminobutyric acid receptors (GABARs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and ...Type A γ-aminobutyric acid receptors (GABARs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABAR pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABAR assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABARs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABAR assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed. #1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2018 タイトル: Real-space refinement in PHENIX for cryo-EM and crystallography. 著者: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / ![]() ![]() ![]() 要旨: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. | |||||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 427.9 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 2.5 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.5 MB | 表示 | |
XML形式データ | ![]() | 72.9 KB | 表示 | |
CIF形式データ | ![]() | 106.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 29742MC ![]() 8foiC ![]() 8g4nC ![]() 8g4oC ![]() 8g4xC ![]() 8g5fC ![]() 8g5hC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-Gamma-aminobutyric acid receptor subunit ... , 4種, 5分子 ABEDC
#1: タンパク質 | 分子量: 51818.516 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() | ||||
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#2: タンパク質 | 分子量: 59265.312 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #3: タンパク質 | | 分子量: 55160.281 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #6: タンパク質 | | 分子量: 55461.684 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
-抗体 , 2種, 2分子 HL
#4: 抗体 | 分子量: 24159.895 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() |
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#5: 抗体 | 分子量: 23624.080 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() |
-糖 , 5種, 8分子 ![](data/chem/img/NAG.gif)
#7: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||||||
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#8: 多糖 | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #9: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #10: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #14: 糖 | ChemComp-NAG / | |
-非ポリマー , 4種, 6分子 ![](data/chem/img/PIO.gif)
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![](data/chem/img/ABU.gif)
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#11: 化合物 | #12: 化合物 | ChemComp-Y4B / | #13: 化合物 | #15: 化合物 | ChemComp-R5R / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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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 |
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試料調製
構成要素 | 名称: Native GABAA Receptor isolated from mouse brain containing one alpha1 subunit, in complex with 8E3-Fab, GABA, Zolpidem, and endogenous neurosteroid タイプ: COMPLEX / Entity ID: #1-#6 / 由来: NATURAL | |||||||||||||||
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分子量 | 値: 0.35 MDa / 実験値: NO | |||||||||||||||
由来(天然) | 生物種: ![]() ![]() | |||||||||||||||
緩衝液 | pH: 8 | |||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: This sample was monodisperse. | |||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/1 | |||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 293 K |
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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: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2100 nm / 最小 デフォーカス(公称値): 800 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) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア | 名称: cryoSPARC / バージョン: 3.3.2 / カテゴリ: 3次元再構成 | ||||||||||||||||||||||||
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: 2.94 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 87268 / アルゴリズム: BACK PROJECTION / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL / 空間: REAL | ||||||||||||||||||||||||
拘束条件 |
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