+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6vxo | ||||||
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タイトル | NaChBac-Nav1.7VSDII chimera in nanodisc | ||||||
要素 | NaChBac-Nav1.7VSDII chimera | ||||||
キーワード | MEMBRANE PROTEIN / NaChBac / Channels / Sodium Ion-Selective | ||||||
機能・相同性 | 機能・相同性情報 detection of mechanical stimulus involved in sensory perception / membrane depolarization during action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain ...detection of mechanical stimulus involved in sensory perception / membrane depolarization during action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain / sodium ion transmembrane transport / sensory perception of pain / post-embryonic development / circadian rhythm / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / inflammatory response / axon / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Bacillus halodurans C-125 (バクテリア) Homo sapiens (ヒト) | ||||||
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: 3.5 Å | ||||||
データ登録者 | Yan, N. / Gao, S. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2020 タイトル: Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na channels in nanodisc. 著者: Shuai Gao / William C Valinsky / Nguyen Cam On / Patrick R Houlihan / Qian Qu / Lei Liu / Xiaojing Pan / David E Clapham / Nieng Yan / 要旨: NaChBac, the first bacterial voltage-gated Na (Na) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Na channels. Discovered nearly ...NaChBac, the first bacterial voltage-gated Na (Na) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Na channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the single particle electron cryomicroscopy (cryo-EM) analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NaAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Na channels in lipid bilayers. To study GMTs in mammalian Na channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Na1.7 replaced the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 and 3.2 Å resolutions, respectively. Compared to the structure of HWTX-IV-bound human Na1.7, which was obtained at an overall resolution of 3.2 Å, the local resolution of the toxin has been improved from ∼6 to ∼4 Å. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Na channels in a membrane environment. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6vxo.cif.gz | 182.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6vxo.ent.gz | 150 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6vxo.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 | 6vxo_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6vxo_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 6vxo_validation.xml.gz | 42 KB | 表示 | |
CIF形式データ | 6vxo_validation.cif.gz | 52 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/vx/6vxo ftp://data.pdbj.org/pub/pdb/validation_reports/vx/6vxo | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 31901.695 Da / 分子数: 4 / 由来タイプ: 組換発現 由来: (組換発現) Bacillus halodurans C-125 (バクテリア), (組換発現) Homo sapiens (ヒト) 株: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 遺伝子: BH1501, SCN9A, NENA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9KCR8, UniProt: Q15858 #2: 化合物 | ChemComp-POV / ( 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 |
-試料調製
構成要素 | 名称: NaChBac-Nav1.7VSDII chimera / タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT | |||||||||||||||
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由来(天然) | 生物種: Bacillus halodurans C-125 (バクテリア) | |||||||||||||||
由来(組換発現) | 生物種: Escherichia coli (大腸菌) | |||||||||||||||
緩衝液 | pH: 8 | |||||||||||||||
緩衝液成分 |
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試料 | 濃度: 5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: NaChBac-Nav1.7VSDII chimera in lipid nanodisc | |||||||||||||||
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: 281 K / 詳細: blot for 5 seconds before plunging |
-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: 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 |
撮影 | 電子線照射量: 53 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17rc2_3619: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 31147 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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