+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1dbh | ||||||
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タイトル | DBL AND PLECKSTRIN HOMOLOGY DOMAINS FROM HSOS1 | ||||||
要素 | PROTEIN (HUMAN SOS 1) | ||||||
キーワード | GENE REGULATION (遺伝子発現の調節) / GUANINE NUCLEOTIDE EXCHANGE FACTOR (グアニンヌクレオチド交換因子) | ||||||
機能・相同性 | 機能・相同性情報 midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / blood vessel morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / epidermal growth factor receptor binding / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / 髄鞘 / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / molecular condensate scaffold activity / NCAM signaling for neurite out-growth / GTPase activator activity / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / guanyl-nucleotide exchange factor activity / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to ischemia / 軸索誘導 / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / multicellular organism growth / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / SH3 domain binding / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / G alpha (12/13) signalling events / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / insulin receptor signaling pathway / regulation of cell population proliferation / RAF/MAP kinase cascade / Ras protein signal transduction / Potential therapeutics for SARS / protein heterodimerization activity / neuronal cell body 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 / 多波長異常分散 / 解像度: 2.3 Å | ||||||
データ登録者 | Soisson, S.M. / Kuriyan, J. | ||||||
引用 | ジャーナル: Cell(Cambridge,Mass.) / 年: 1998 タイトル: Crystal structure of the Dbl and pleckstrin homology domains from the human Son of sevenless protein. 著者: Soisson, S.M. / Nimnual, A.S. / Uy, M. / Bar-Sagi, D. / Kuriyan, 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 | 1dbh.cif.gz | 80.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1dbh.ent.gz | 63.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1dbh.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/db/1dbh ftp://data.pdbj.org/pub/pdb/validation_reports/db/1dbh | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 41312.812 Da / 分子数: 1 / 断片: DBL AND PLECKSTRIN HOMOLOGY DOMAINS / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: Q07889 |
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#2: 水 | ChemComp-HOH / |
-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: 3.21 Å3/Da / 溶媒含有率: 62 % 解説: SELENOMETHIONINE MAD DATA WERE COLLECTED USING INVERSE-BEAM GEOMETRY | ||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 6.5 詳細: 5 MG/ML PROTEIN 100 MM BIS-TRIS PH 6.5 1-3% PEG6000 1 MM DTT | ||||||||||||||||||||||||||||||||||||
結晶 | *PLUS | ||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 20 ℃ / 手法: 蒸気拡散法, シッティングドロップ法 | ||||||||||||||||||||||||||||||||||||
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: NSLS / ビームライン: X4A / 波長: 0.9686, 0.9792, 0.9794, 0.9856 | |||||||||||||||
検出器 | タイプ: RIGAKU RAXIS / 検出器: IMAGE PLATE | |||||||||||||||
放射 | プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray | |||||||||||||||
放射波長 |
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反射 | 解像度: 2.3→30 Å / Num. obs: 23805 / % possible obs: 99 % / 冗長度: 19 % / Rsym value: 0.036 / Net I/σ(I): 21.1 | |||||||||||||||
反射 シェル | 解像度: 2.3→2.4 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.187 / % possible all: 96.9 | |||||||||||||||
反射 | *PLUS Num. measured all: 238642 / Rmerge(I) obs: 0.036 | |||||||||||||||
反射 シェル | *PLUS % possible obs: 96.9 % / Rmerge(I) obs: 0.187 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 2.3→30 Å / Data cutoff high rms absF: 1000000 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 詳細: DISORDERED SIDE CHAIN ATOM OCCUPANCIES WERE SET TO ZERO
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溶媒の処理 | 溶媒モデル: DENSITY MODIFICATION / Bsol: 45.4 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 44.7 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.3→30 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.3→2.32 Å / Total num. of bins used: 47 /
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Xplor file |
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ソフトウェア | *PLUS 名称: 'CNS CNS-03' / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.3 Å / 最低解像度: 30 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 44.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.319 / Rfactor Rwork: 0.274 |