+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2ka9 | ||||||
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タイトル | Solution structure of PSD-95 PDZ12 complexed with cypin peptide | ||||||
要素 |
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キーワード | CELL ADHESION (細胞接着) / PDZ-cypin peptide complex / tandem PDZ domain / Alternative splicing (選択的スプライシング) / Cell junction (細胞結合) / Cell membrane (細胞膜) / Lipoprotein (リポタンパク質) / Membrane (生体膜) / Palmitate (パルミチン酸) / Phosphoprotein / Postsynaptic cell membrane / SH3 domain (SH3ドメイン) / Synapse (シナプス) | ||||||
機能・相同性 | 機能・相同性情報 RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / 胚 / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / 胚 / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / receptor localization to synapse / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / 樹状突起 / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / juxtaparanode region of axon / dendritic spine morphogenesis / negative regulation of receptor internalization / frizzled binding / neuron projection terminus / dendritic spine organization / postsynaptic neurotransmitter receptor diffusion trapping / acetylcholine receptor binding / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / regulation of NMDA receptor activity / beta-2 adrenergic receptor binding / cortical cytoskeleton / regulation of neuronal synaptic plasticity / locomotory exploration behavior / social behavior / kinesin binding / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / positive regulation of protein tyrosine kinase activity / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / extrinsic component of cytoplasmic side of plasma membrane / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cerebral cortex development / kinase binding / 細胞接着 / cell-cell junction / シナプス小胞 / 細胞結合 / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / postsynapse / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / protein-containing complex assembly / 樹状突起スパイン / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / シナプス / 樹状突起 / protein-containing complex binding / protein kinase binding / 小胞体 / 生体膜 / 細胞膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||
手法 | 溶液NMR / simulated annealing | ||||||
データ登録者 | Wang, W.N. / Weng, J.W. / Zhang, X. / Liu, M.L. / Zhang, M.J. | ||||||
引用 | ジャーナル: J.Am.Chem.Soc. / 年: 2009 タイトル: Creating conformational entropy by increasing interdomain mobility in ligand binding regulation: a revisit to N-terminal tandem PDZ domains of PSD-95 著者: Wang, W.N. / Weng, J.W. / Zhang, X. / Liu, M.L. / Zhang, M.J. | ||||||
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 | 2ka9.cif.gz | 1.2 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2ka9.ent.gz | 1017.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2ka9.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/ka/2ka9 ftp://data.pdbj.org/pub/pdb/validation_reports/ka/2ka9 | 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: 20126.957 Da / 分子数: 1 / 断片: N-terminal PDZ12 domain / 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: Dlg4, Dlgh4, Psd95 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P31016 |
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#2: タンパク質・ペプチド | 分子量: 949.058 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: synthetic peptide |
-実験情報
-実験
実験 | 手法: 溶液NMR |
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NMR実験 | タイプ: 3D 15N-separated NOESY |
-試料調製
詳細 | 内容: 1mM [U-15N] PSD95 PDZ12, 1mM cypin peptide, 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: 100 / pH: 6.5 / 圧: ambient / 温度: 303 K |
-NMR測定
NMRスペクトロメーター |
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-解析
NMR software | 名称: CNS / 分類: 精密化 |
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精密化 | 手法: simulated annealing / ソフトェア番号: 1 詳細: This structure is not superimposed because the relative domain orientation is not defined due to its intrinsic conformational flexibility. |
NMR constraints | NOE constraints total: 3564 |
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: 200 / 登録したコンフォーマーの数: 20 / 代表コンフォーマー: 1 |
NMR ensemble rms | Bond angle rms dev: 0.393 ° / Covalent bond rms dev: 0.0021 Å / Dihedral angles rms dev: 29.297 ° / Improper torsion angle rms dev: 0.287 ° |