+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7zrq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | 1.68 Angstrom crystal structure of Ca/CaM-E140G:CaMKIIdelta peptide complex | |||||||||
要素 |
| |||||||||
キーワード | METAL BINDING PROTEIN / calcium-binding protein / calmodulin / CaM / CaMKII / kinase | |||||||||
機能・相同性 | 機能・相同性情報 regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / calcium- and calmodulin-dependent protein kinase complex / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / calcium- and calmodulin-dependent protein kinase complex / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction / Trafficking of AMPA receptors / endoplasmic reticulum calcium ion homeostasis / cardiac muscle cell contraction / Assembly and cell surface presentation of NMDA receptors / sodium channel inhibitor activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / relaxation of cardiac muscle / Calmodulin induced events / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / Reduction of cytosolic Ca++ levels / calcium/calmodulin-dependent protein kinase activity / 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 / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of heart contraction / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / 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 / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / HSF1-dependent transactivation / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / sarcoplasmic reticulum membrane / 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 / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.68 Å | |||||||||
データ登録者 | Helassa, N. / Antonyuk, S. | |||||||||
資金援助 | 英国, 2件
| |||||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2022 タイトル: Calmodulin variant E140G associated with long QT syndrome impairs CaMKII delta autophosphorylation and L-type calcium channel inactivation. 著者: Prakash, O. / Gupta, N. / Milburn, A. / McCormick, L. / Deugi, V. / Fisch, P. / Wyles, J. / Thomas, N.L. / Antonyuk, S. / Dart, C. / Helassa, N. | |||||||||
履歴 |
|
-構造の表示
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 | 7zrq.cif.gz | 79.8 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb7zrq.ent.gz | 57.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7zrq.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/zr/7zrq ftp://data.pdbj.org/pub/pdb/validation_reports/zr/7zrq | HTTPS FTP |
---|
-関連構造データ
関連構造データ | 7zrpC 2welS S: 精密化の開始モデル C: 同じ文献を引用 (文献) |
---|---|
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 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-要素
#1: タンパク質 | 分子量: 16649.287 Da / 分子数: 1 / 変異: E140G / 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: Escherichia coli (大腸菌) / 参照: UniProt: P0DP23 | ||||||
---|---|---|---|---|---|---|---|
#2: タンパク質・ペプチド | 分子量: 2515.011 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) 参照: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase | ||||||
#3: 化合物 | ChemComp-CA / #4: 化合物 | ChemComp-GOL / | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
---|
-試料調製
結晶 | 溶媒含有率: 27.04 % |
---|---|
結晶化 | 温度: 292 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 0.1 M Na+-HEPES, 0.1 M MOPS (acid), pH 7.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
---|---|
放射光源 | 由来: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.9795 Å |
検出器 | タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年12月11日 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.9795 Å / 相対比: 1 |
反射 | 解像度: 1.68→39.59 Å / Num. obs: 15287 / % possible obs: 99.1 % / 冗長度: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Net I/σ(I): 13.5 |
反射 シェル | 解像度: 1.68→1.71 Å / 冗長度: 4.6 % / Rmerge(I) obs: 2.042 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 684 / CC1/2: 0.311 / Rpim(I) all: 1.452 / Rrim(I) all: 2.522 / % possible all: 87.8 |
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: 2WEL 解像度: 1.68→39.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 9.797 / SU ML: 0.136 / 交差検証法: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 / 詳細: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 29.842 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.68→39.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 TLSグループ | Selection: ALL |