PDB-8eow: Eag Kv channel with voltage sensor in the up conformation

基本情報

• 登録情報: データベース: PDB / ID: 8eow
• タイトル: Eag Kv channel with voltage sensor in the up conformation

要素

• Calmodulin-1カルモジュリン
• Potassium voltage-gated channel subfamily H member 1

• キーワード: MEMBRANE PROTEIN (膜タンパク質) / voltage-gated potassium channel

機能・相同性

分子機能:

Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / CAM型光合成 / parallel fiber to Purkinje cell synapse / Cam-PDE 1 activation / Sodium/Calcium exchangers / nuclear inner membrane / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / phosphatidylinositol bisphosphate binding / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / startle response / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / 長期増強 / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / axolemma / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / potassium ion transmembrane transport / voltage-gated potassium channel complex / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / monoatomic ion transmembrane transport / sperm midpiece / 14-3-3 protein binding / calcium channel complex / substantia nigra development / cellular response to calcium ion / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of membrane potential / Translocation of SLC2A4 (GLUT4) to the plasma membrane / postsynaptic density membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / Stimuli-sensing channels / cellular response to type II interferon / 紡錘体 / response to calcium ion

ドメイン・相同性:

Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair

構成要素:

Calmodulin-1 / Potassium voltage-gated channel subfamily H member 1

• 生物種: Rattus norvegicus (ドブネズミ); 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: 3.9 Å
• データ登録者: Mandala, V.S. / MacKinnon, R.

資金援助

米国, 1件

組織	認可番号	国
Howard Hughes Medical Institute (HHMI)		米国

• 引用: ジャーナル: Proc Natl Acad Sci U S A / 年: 2022; タイトル: Voltage-sensor movements in the Eag Kv channel under an applied electric field.; 著者: Venkata Shiva Mandala / Roderick MacKinnon / ; 要旨: Voltage-dependent ion channels regulate the opening of their pores by sensing the membrane voltage. This process underlies the propagation of action potentials and other forms of electrical activity in cells. The voltage dependence of these channels is governed by the transmembrane displacement of the positive charged S4 helix within their voltage-sensor domains. We use cryo-electron microscopy to visualize this movement in the mammalian Eag voltage-dependent potassium channel in lipid membrane vesicles with a voltage difference across the membrane. Multiple structural configurations show that the applied electric field displaces S4 toward the cytoplasm by two helical turns, resulting in an extended interfacial helix near the inner membrane leaflet. The position of S4 in this down conformation is sterically incompatible with an open pore, thus explaining how movement of the voltage sensor at hyperpolarizing membrane voltages locks the pore shut in this kind of voltage-dependent K (K) channel. The structures solved in lipid bilayer vesicles detail the intricate interplay between K channels and membranes, from showing how arginines are stabilized deep within the membrane and near phospholipid headgroups, to demonstrating how the channel reshapes the inner leaflet of the membrane itself.

履歴

登録	2022年10月4日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2022年11月16日	Provider: repository / タイプ: Initial release

集合体

登録構造単位

A: Potassium voltage-gated channel subfamily H member 1

E: Calmodulin-1

D: Potassium voltage-gated channel subfamily H member 1

C: Potassium voltage-gated channel subfamily H member 1

B: Potassium voltage-gated channel subfamily H member 1

H: Calmodulin-1

G: Calmodulin-1

F: Calmodulin-1

概要:

• 391 kDa, 8 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	390,911	8
ポリマ－	390,911	8
非ポリマー	0	0
水	0

1

概要:

• 登録構造と同一
• 登録者が定義した集合体
• 根拠: gel filtration, Stable complex: co-elutes on gel filtration

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555		1

要素

#1: タンパク質

A D C B
Potassium voltage-gated channel subfamily H member 1 / Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / r-eag / Voltage-gated potassium channel subunit Kv10.1

詳細:

分子量: 81664.094 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: Kcnh1, Eag / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q63472

#2: タンパク質

E H G F
Calmodulin-1 / カルモジュリン

詳細:

分子量: 16063.608 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: CALM1, CALM, CAM, CAM1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DP23

実験情報

実験

• 実験: 手法: 電子顕微鏡法
• 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: Complex of Eag Kv channel bound to the inhibitor calmodulin-Ca2+; タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES
• 分子量: 実験値: NO

由来(天然)

ID	Entity assembly-ID	生物種	Ncbi tax-ID
2	1	Rattus norvegicus (ドブネズミ)	10116
3	1	Homo sapiens (ヒト)	9606

• 由来(組換発現): 生物種: Homo sapiens (ヒト)
• 緩衝液: pH: 8
• 試料: 濃度: 0.2 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: GOLD / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3
• 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

電子顕微鏡撮影

• 実験機器: モデル: Titan Krios / 画像提供: FEI Company
• 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 FIELDBright-field microscopy / 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: 60 e/Ų; フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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
• CTF補正: タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
• 対称性: 点対称性: C₄ (4回回転対称)
• 3次元再構成: 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 49164 / 対称性のタイプ: POINT

拘束条件

Refine-ID	タイプ	Dev ideal	数
ELECTRON MICROSCOPY	f_bond_d	0.003	25188
ELECTRON MICROSCOPY	f_angle_d	0.554	34444
ELECTRON MICROSCOPY	f_dihedral_angle_d	3.594	3588
ELECTRON MICROSCOPY	f_chiral_restr	0.039	4052
ELECTRON MICROSCOPY	f_plane_restr	0.003	4420