+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1gmo | ||||||||||||
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タイトル | CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR | ||||||||||||
要素 | HEPATOCYTE GROWTH FACTOR | ||||||||||||
キーワード | HORMONE / GROWTH FACTOR | ||||||||||||
機能・相同性 | 機能・相同性情報 regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / chemoattractant activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / epithelial cell proliferation / Interleukin-7 signaling / negative regulation of autophagy / cell chemotaxis / platelet alpha granule lumen / liver development / negative regulation of inflammatory response / growth factor activity / cell morphogenesis / Negative regulation of MET activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / Platelet degranulation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane 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: 3 Å | ||||||||||||
データ登録者 | Lietha, D. / Chirgadze, D.Y. / Mulloy, B. / Blundell, T.L. / Gherardi, E. | ||||||||||||
引用 | ジャーナル: Embo J. / 年: 2001 タイトル: Crystal Structures of Nk1-Heparin Complexes Reveal the Basis for Nk1 Activity and Enable Engineering of Potent Agonists of the met Receptor 著者: Lietha, D. / Chirgadze, D.Y. / Mulloy, B. / Blundell, T.L. / Gherardi, E. | ||||||||||||
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 | 1gmo.cif.gz | 294.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1gmo.ent.gz | 242.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1gmo.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
文書・要旨 | 1gmo_validation.pdf.gz | 2.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1gmo_full_validation.pdf.gz | 2.3 MB | 表示 | |
XML形式データ | 1gmo_validation.xml.gz | 66.4 KB | 表示 | |
CIF形式データ | 1gmo_validation.cif.gz | 87.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/gm/1gmo ftp://data.pdbj.org/pub/pdb/validation_reports/gm/1gmo | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
-タンパク質 , 1種, 8分子 ABCDEFGH
#1: タンパク質 | 分子量: 21173.260 Da / 分子数: 8 / 断片: NK1 / 変異: YES / 由来タイプ: 組換発現 / 詳細: NK1 DIMER IN COMPLEX WITH HEPARIN MOLECULE / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PPIC-9K / 発現宿主: PICHIA PASTORIS (菌類) / 株 (発現宿主): GS115 / 参照: UniProt: P14210 |
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-糖 , 5種, 6分子
#2: 多糖 | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid |
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#3: 多糖 | 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid |
#4: 多糖 | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid |
#5: 多糖 | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose |
#6: 多糖 |
-非ポリマー , 3種, 199分子
#7: 化合物 | ChemComp-SO4 / #8: 化合物 | ChemComp-EPE / #9: 水 | ChemComp-HOH / | |
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-詳細
構成要素の詳細 | ENGINEERED RESIDUE IN CHAIN A, ALA 29 TO VAL ENGINEERED RESIDUE IN CHAIN A, ASN 72 TO ASP ...ENGINEERED |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.43 Å3/Da / 溶媒含有率: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7.5 詳細: 10% PEG4000, 8% ETHYLENE GLYCOL, 0.10M SODIUM PARA-TOLUENE SULFONATE,0.10M SODIUM HEPES, PH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 8.5 / 手法: 蒸気拡散法, ハンギングドロップ法 | ||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: SRS / ビームライン: PX14.2 / 波長: 0.979 |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2000年2月17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: 0.979 Å / 相対比: 1 |
反射 | 解像度: 2.95→20 Å / Num. obs: 37651 / % possible obs: 95.2 % / Observed criterion σ(I): 3 / 冗長度: 6 % / Biso Wilson estimate: 78.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12 |
反射 シェル | 解像度: 2.95→3.02 Å / Rmerge(I) obs: 0.327 / % possible all: 91.4 |
反射 | *PLUS 最低解像度: 20 Å |
反射 シェル | *PLUS % possible obs: 91.4 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRIES 1NK1 AND 1BHT 解像度: 3→20 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 詳細: BULK SOLVENT MODEL USED
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 22.6753 Å2 / ksol: 0.28727 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 60.4 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 3→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3→3.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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