+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7zdz | ||||||||||||
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タイトル | Cryo-EM structure of the human inward-rectifier potassium 2.1 channel (Kir2.1) | ||||||||||||
要素 | Inward rectifier potassium channel 2 | ||||||||||||
キーワード | MEMBRANE PROTEIN / Potassium channel / Inward-rectifier channel / inward rectification | ||||||||||||
機能・相同性 | 機能・相同性情報 Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / membrane repolarization during cardiac muscle cell action potential / regulation of resting membrane potential ...Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / membrane repolarization during cardiac muscle cell action potential / regulation of resting membrane potential / regulation of membrane repolarization / positive regulation of potassium ion transmembrane transport / membrane depolarization during cardiac muscle cell action potential / intracellular potassium ion homeostasis / inward rectifier potassium channel activity / cardiac muscle cell action potential involved in contraction / regulation of cardiac muscle cell contraction / regulation of monoatomic ion transmembrane transport / relaxation of cardiac muscle / regulation of heart rate by cardiac conduction / potassium ion import across plasma membrane / intercalated disc / smooth endoplasmic reticulum / rough endoplasmic reticulum / voltage-gated potassium channel complex / potassium ion transmembrane transport / T-tubule / phosphatidylinositol-4,5-bisphosphate binding / potassium ion transport / cellular response to mechanical stimulus / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / postsynaptic membrane / protein homotetramerization / dendritic spine / neuronal cell body / glutamatergic synapse / Golgi apparatus / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | 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: 4.3 Å | ||||||||||||
データ登録者 | Fernandes, C.A.H. / Venien-Bryan, C. / Fagnen, C. / Zuniga, D. | ||||||||||||
資金援助 | フランス, 3件
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引用 | ジャーナル: Sci Adv / 年: 2022 タイトル: Cryo-electron microscopy unveils unique structural features of the human Kir2.1 channel. 著者: Carlos A H Fernandes / Dania Zuniga / Charline Fagnen / Valérie Kugler / Rosa Scala / Gérard Péhau-Arnaudet / Renaud Wagner / David Perahia / Saïd Bendahhou / Catherine Vénien-Bryan / 要旨: We present the first structure of the human Kir2.1 channel containing both transmembrane domain (TMD) and cytoplasmic domain (CTD). Kir2.1 channels are strongly inward-rectifying potassium channels ...We present the first structure of the human Kir2.1 channel containing both transmembrane domain (TMD) and cytoplasmic domain (CTD). Kir2.1 channels are strongly inward-rectifying potassium channels that play a key role in maintaining resting membrane potential. Their gating is modulated by phosphatidylinositol 4,5-bisphosphate (PIP). Genetically inherited defects in Kir2.1 channels are responsible for several rare human diseases, including Andersen's syndrome. The structural analysis (cryo-electron microscopy), surface plasmon resonance, and electrophysiological experiments revealed a well-connected network of interactions between the PIP-binding site and the G-loop through residues R312 and H221. In addition, molecular dynamics simulations and normal mode analysis showed the intrinsic tendency of the CTD to tether to the TMD and a movement of the secondary anionic binding site to the membrane even without PIP. Our results revealed structural features unique to human Kir2.1 and provided insights into the connection between G-loop and gating and the pathological mechanisms associated with this 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 | 7zdz.cif.gz | 235.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7zdz.ent.gz | 192.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7zdz.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 | 7zdz_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7zdz_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 7zdz_validation.xml.gz | 203.7 KB | 表示 | |
CIF形式データ | 7zdz_validation.cif.gz | 569.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/zd/7zdz ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zdz | HTTPS FTP |
-関連構造データ
関連構造データ | 14678MC 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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-要素
#1: タンパク質 | 分子量: 48344.141 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KCNJ2, IRK1 / 発現宿主: Komagataella pastoris (菌類) / 参照: UniProt: P63252 #2: 化合物 | ChemComp-K / | #3: 化合物 | 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: Human inward-rectifier potassium channel 2.1 (Kir2.1) タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / 由来: RECOMBINANT | ||||||||||||||||||||||||||||||
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分子量 | 値: 50 kDa/nm / 実験値: YES | ||||||||||||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | ||||||||||||||||||||||||||||||
由来(組換発現) | 生物種: Komagataella pastoris (菌類) | ||||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.6 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-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 / 倍率(公称値): 105000 X / 最大 デフォーカス(公称値): 2800 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2.7 mm / C2レンズ絞り径: 100 µm / アライメント法: BASIC |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 4 sec. / 電子線照射量: 61.7 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 撮影したグリッド数: 1 / 実像数: 9895 |
画像スキャン | サンプリングサイズ: 10 µm / 横: 5760 / 縦: 4092 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1031472 | ||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 63584 / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 404.73 / プロトコル: OTHER / 空間: REAL / Target criteria: Correlation coefficient 詳細: For structural fitting, it was used dock-in-map (available at PHENIX) that uses both SSM and convolution-based shape searches to find a part of a map that is similar to a model. An initial in ...詳細: For structural fitting, it was used dock-in-map (available at PHENIX) that uses both SSM and convolution-based shape searches to find a part of a map that is similar to a model. An initial in silico homology model of human Kir2.1 was generated using I-TASSER using the crystal structure of chicken Kir2.2 channel (PDB ID 3JYC) as a template. For building and refinement of the atomic model, the transmembrane domain (TMD, 55-184 region) of this in silico model was placed into the final sharpened cryo-EM map using the Dock in Map tool available in PHENIX. For the cytoplasmic domain (CTD; 188-367 region), the crystal structure of the CTD from mice Kir2.1 channel (PDB ID 1U4F) was placed into the final cryo-EM map using the same approach. Once the models were placed in the electron density, the loops that connect the two domains (185-187 region) and a N-terminal loop (41-54 region) absent in the in silico model were manually built using Coot. | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 1U4F Pdb chain residue range: 188-367 | ||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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