+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2kle | ||||||
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タイトル | ISIC Refined Solution Structure of the Calcium Binding Domain of the C-terminal Cytosolic Domain of Polycystin-2 | ||||||
要素 | Polycystin-2 | ||||||
キーワード | MEMBRANE PROTEIN / PC2 / PKD2 / Calcium binding domain / EF hand / Cytosolic / Calcium / Coiled coil / Disease mutation / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Polymorphism / Transmembrane / Transport | ||||||
機能・相同性 | 機能・相同性情報 detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / centrosome duplication / detection of mechanical stimulus / calcium-induced calcium release activity / regulation of calcium ion import / cation channel complex / muscle alpha-actinin binding / placenta blood vessel development / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / cellular response to fluid shear stress / voltage-gated monoatomic cation channel activity / cellular response to osmotic stress / non-motile cilium / actinin binding / motile cilium / transcription regulator inhibitor activity / determination of left/right symmetry / aorta development / inorganic cation transmembrane transport / neural tube development / ciliary membrane / voltage-gated sodium channel activity / protein heterotetramerization / embryonic placenta development / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated potassium channel activity / cytoplasmic side of endoplasmic reticulum membrane / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / sodium ion transmembrane transport / voltage-gated calcium channel activity / monoatomic cation channel activity / basal plasma membrane / cellular response to cAMP / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / cytoskeletal protein binding / cellular response to calcium ion / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / calcium ion transmembrane transport / protein tetramerization / cellular response to reactive oxygen species / cytoplasmic vesicle membrane / cilium / mitotic spindle / Wnt signaling pathway / intracellular calcium ion homeostasis / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / ATPase binding / heart development / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / cell surface receptor signaling pathway / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 溶液NMR / restrained molecular dynamics, simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
データ登録者 | Kalbitzer, H.R. | ||||||
引用 | ジャーナル: Biomol.Nmr Assign. / 年: 2009 タイトル: NMR-assignments of a cytosolic domain of the C-terminus of polycystin-2 著者: Schumann, F.H. / Hoffmeister, H. / Schmidt, M. / Bader, R. / Besl, E. / Witzgall, R. / Kalbitzer, H.R. #1: ジャーナル: J.Biol.Chem. / 年: 2009 タイトル: Ca2+-dependent conformational changes in a C-terminal cytosolic domain of polycystin-2 著者: Schumann, F. / Hoffmeister, H. / Bader, R. / Schmidt, M. / Witzgall, R. / Kalbitzer, H.R. | ||||||
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 | 2kle.cif.gz | 233.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2kle.ent.gz | 188.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2kle.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/kl/2kle ftp://data.pdbj.org/pub/pdb/validation_reports/kl/2kle | HTTPS FTP |
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-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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NMR アンサンブル |
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-要素
#1: タンパク質 | 分子量: 14024.415 Da / 分子数: 1 / 断片: residues 680-796 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PKD2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13563 |
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-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR実験 |
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-試料調製
詳細 | 内容: 0.5mM [U-100% 13C; U-100% 15N] Polycystin-2 Polypeptide-1, 5mM Ca2+-2, 0.1mM DSS-3, 10mM potassium phosphate buffer-4, 500mM NaCl-5, 2mM DTE-6, 90% H2O/10% D2O 溶媒系: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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試料 |
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試料状態 | イオン強度: 0.51 / pH: 6.8 / 圧: ambient / 温度: 293 K |
-NMR測定
NMRスペクトロメーター |
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-解析
NMR software |
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精密化 | 手法: restrained molecular dynamics, simulated annealing / ソフトェア番号: 1 詳細: THE STRUCTURES WERE FIRST REFINED WITH AUREMOL-ISUC AND THEN REFINED WITH CNS IN EXPLICIT WATER; Brunner, K., Gronwald, W., Trenner, J.M., Neidig, K.P., and Kalbitzer, H.R. (2006) BMC Struct. ...詳細: THE STRUCTURES WERE FIRST REFINED WITH AUREMOL-ISUC AND THEN REFINED WITH CNS IN EXPLICIT WATER; Brunner, K., Gronwald, W., Trenner, J.M., Neidig, K.P., and Kalbitzer, H.R. (2006) BMC Struct. Biol. 6, 14, for Waterre finement; Linge, J.P., Williams, M.A., Spronk, C.A.E.M., Bonvin, A.M.J.J. & Nilges, M. (2003). Refinement of protein structures in explicit solvent. Proteins: Struct. Funct. Genet. 50, 496-506 for EXPLICIT WATER refinement | ||||||||||||||||||||||||
代表構造 | 選択基準: lowest energy | ||||||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 1000 / 登録したコンフォーマーの数: 10 / 代表コンフォーマー: 1 |