+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8vc3 | ||||||
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タイトル | Voltage gated potassium ion channel Kv1.2 in complex with DTx | ||||||
要素 |
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キーワード | MEMBRANE PROTEIN / Ion Channel / Toxin bound / Blocker | ||||||
機能・相同性 | 機能・相同性情報 optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / axon initial segment / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / axon initial segment / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / juxtaparanode region of axon / optic nerve development / regulation of dopamine secretion / neuronal cell body membrane / action potential / kinesin binding / lamellipodium membrane / calyx of Held / voltage-gated potassium channel activity / neuronal action potential / potassium channel regulator activity / voltage-gated potassium channel complex / axon terminus / potassium ion transmembrane transport / sensory perception of pain / serine-type endopeptidase inhibitor activity / protein homooligomerization / cerebral cortex development / lamellipodium / presynaptic membrane / toxin activity / perikaryon / postsynaptic membrane / endosome / axon / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / extracellular space / membrane / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) Dendroaspis angusticeps (コブラ) | ||||||
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: 3.2 Å | ||||||
データ登録者 | Wu, Y. / Sigworth, F.J. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: bioRxiv / 年: 2024 タイトル: Cryo-EM structures of Kv1.2 potassium channels, conducting and non-conducting. 著者: Yangyu Wu / Yangyang Yan / Youshan Yang / Shumin Bian / Alberto Rivetta / Ken Allen / Fred J Sigworth / 要旨: We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 Å, 2.5 Å, 3.2 ...We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 Å, 2.5 Å, 3.2 Å, and 2.9Å. These structures, all obtained at nominally zero membrane potential in detergent micelles, reveal distinct ion-occupancy patterns in the selectivity filter. The first two structures are very similar to those reported in the related Shaker channel and the much-studied Kv1.2-2.1 chimeric channel. On the other hand, two new structures show unexpected patterns of ion occupancy. First, the toxin α-Dendrotoxin, like Charybdotoxin, is seen to attach to the negatively-charged channel outer mouth, and a lysine residue penetrates into the selectivity filter, with the terminal amine coordinated by carbonyls, partially disrupting the outermost ion-binding site. In the remainder of the filter two densities of bound ions are observed, rather than three as observed with other toxin-blocked Kv channels. Second, a structure of Kv1.2 in Na solution does not show collapse or destabilization of the selectivity filter, but instead shows an intact selectivity filter with ion density in each binding site. We also attempted to image the C-type inactivated Kv1.2 W366F channel in Na solution, but the protein conformation was seen to be highly variable and only a low-resolution structure could be obtained. These findings present new insights into the stability of the selectivity filter and the mechanism of toxin block of this intensively studied, voltage-gated potassium channel. | ||||||
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 | 8vc3.cif.gz | 277.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8vc3.ent.gz | 172.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8vc3.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 | 8vc3_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8vc3_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 8vc3_validation.xml.gz | 42.6 KB | 表示 | |
CIF形式データ | 8vc3_validation.cif.gz | 63 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/vc/8vc3 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/8vc3 | 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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1 |
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-要素
#1: タンパク質 | 分子量: 7015.129 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Dendroaspis angusticeps (コブラ) / 参照: UniProt: P00980 | ||||||
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#2: タンパク質 | 分子量: 60591.570 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: Kcna2 / 発現宿主: Komagataella pastoris (菌類) / 参照: UniProt: P63142 #3: 化合物 | 研究の焦点であるリガンドがあるか | Y | Has protein modification | Y | |
-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: Voltage gated potassium channel Kv1.2 with DTx bound タイプ: CELL / Entity ID: #1-#2 / 由来: MULTIPLE SOURCES |
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由来(天然) | 生物種: Komagataella pastoris (菌類) / 株: SMD1168 |
緩衝液 | pH: 7.4 |
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 |
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: 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 / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 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 (6k x 4k) |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.21rc1_5107: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 312202 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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