+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2kol | ||||||
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タイトル | Solution structure of human SDF1-alpha H25R | ||||||
要素 | Stromal cell-derived factor 1CXCL12 | ||||||
キーワード | CYTOKINE (サイトカイン) / chemokine (ケモカイン) / SDF1-alpha / Chemotaxis (走化性) / Growth factor (成長因子) | ||||||
機能・相同性 | 機能・相同性情報 chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / 循環器 / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / Nuclear signaling by ERBB4 / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / cell chemotaxis / adult locomotory behavior / 軸索誘導 / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / 走化性 / integrin binding / G alpha (i) signalling events / collagen-containing extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / 細胞接着 / 免疫応答 / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / シグナル伝達 / extracellular exosome / extracellular region 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 溶液NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | ||||||
Model details | lowest energy, model 1 | ||||||
データ登録者 | Volkman, B.F. / Ziarek, J.J. / Peterson, F.C. / Veldkamp, C.T. | ||||||
引用 | ジャーナル: To be Published タイトル: Solution structure of human SDF1-alpha H25R 著者: Ziarek, J.J. / Veldkamp, C.T. / Peterson, F.C. / Volkman, B.F. | ||||||
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 | 2kol.cif.gz | 491.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2kol.ent.gz | 416.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2kol.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/ko/2kol ftp://data.pdbj.org/pub/pdb/validation_reports/ko/2kol | HTTPS FTP |
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-関連構造データ
類似構造データ | |
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その他のデータベース |
-リンク
-集合体
登録構造単位 |
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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: 7997.507 Da / 分子数: 1 / 断片: SDF-1-alpha, residues 22-89 / 変異: H25R / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CXCL12, SDF1, SDF1A, SDF1B / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): SG130099[pREP4] / 参照: UniProt: P48061 |
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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: 3.3 mM [U-100% 13C; U-100% 15N] SDF1a H25R, 25 mM [U-99% 2H] MES, 0.02 % sodium azide, 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: 20 / pH: 6.8 / 圧: AMBIENT / 温度: 298 K |
-NMR測定
NMRスペクトロメーター | タイプ: Bruker DRX / 製造業者: Bruker / モデル: DRX / 磁場強度: 600 MHz |
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-解析
NMR software |
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精密化 | 手法: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT ソフトェア番号: 1 詳細: STRUCTURES ARE BASED ON A TOTAL OF 1430 NOE CONSTRAINTS (339 INTRA, 388 SEQUENTIAL, 263 MEDIUM, AND 440 LONG RANGE) AND 65 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1430 / NOE intraresidue total count: 339 / NOE long range total count: 440 / NOE medium range total count: 263 / NOE sequential total count: 388 | ||||||||||||||||||||||||||||||||
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: target function / 計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 20 |