+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1mfg | ||||||
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タイトル | The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / PDZ DOMAIN / PROTEIN-PEPTIDE COMPLEX / ERB-B2 / ERBIN. | ||||||
機能・相同性 | 機能・相同性情報 basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / postsynaptic specialization / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / PLCG1 events in ERBB2 signaling / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / postsynaptic specialization / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / PLCG1 events in ERBB2 signaling / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / ERBB2-EGFR signaling pathway / intermediate filament cytoskeleton organization / ERBB2 Activates PTK6 Signaling / semaphorin receptor complex / negative regulation of monocyte chemotactic protein-1 production / regulation of microtubule-based process / ErbB-3 class receptor binding / establishment or maintenance of epithelial cell apical/basal polarity / ERBB2 Regulates Cell Motility / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / PI3K events in ERBB2 signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of Rho protein signal transduction / negative regulation of NF-kappaB transcription factor activity / RHOB GTPase cycle / neuromuscular junction development / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / ERBB2-ERBB3 signaling pathway / positive regulation of transcription by RNA polymerase I / RHOC GTPase cycle / oligodendrocyte differentiation / regulation of postsynaptic membrane neurotransmitter receptor levels / response to muramyl dipeptide / semaphorin-plexin signaling pathway / cellular response to epidermal growth factor stimulus / Signaling by ERBB2 / positive regulation of cell adhesion / RHOG GTPase cycle / basement membrane / RHOA GTPase cycle / positive regulation of protein targeting to membrane / RAC2 GTPase cycle / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / RAC3 GTPase cycle / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / protein targeting / regulation of angiogenesis / neurogenesis / SHC1 events in ERBB2 signaling / coreceptor activity / regulation of ERK1 and ERK2 cascade / Schwann cell development / basal plasma membrane / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / RAC1 GTPase cycle / myelination / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Downregulation of ERBB2:ERBB3 signaling / Constitutive Signaling by Overexpressed ERBB2 / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / integrin-mediated signaling pathway / positive regulation of translation / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / ruffle membrane / wound healing / neuromuscular junction / peptidyl-tyrosine phosphorylation / neuron differentiation / transmembrane signaling receptor activity / structural constituent of cytoskeleton / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / cell junction / PIP3 activates AKT signaling / myelin sheath / cellular response to tumor necrosis factor / presynaptic membrane / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling 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: 1.25 Å | ||||||
データ登録者 | Birrane, G. / Chung, J. / Ladias, J.A. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2003 タイトル: Novel mode of ligand recognition by the erbin PDZ domain 著者: Birrane, G. / Chung, J. / Ladias, J.A. #1: ジャーナル: NAT.CELL BIOL. / 年: 2000 タイトル: BIN: A BASOLATERAL PDZ PROTEIN THAT INTERACTS WITH THE MAMMALIAN ERBB2/HER2 RECEPTOR 著者: BORG, J.P. / MARCHETTO, S. / LEBIVIC, A. / OLLENDORFF, V. / JAULIN-BASTARD, F. / SAITO, H. / FOURNIER, E. / ADELAIDE, J. / MARGOLIS, B. / BIRNBAUM, D. #2: ジャーナル: J.Biol.Chem. / 年: 2002 タイトル: THE ERBIN PDZ DOMAIN BINDS WITH HIGH AFFINITY AND SPECIFICITY TO THE CARBOXYL TERMINI OF DELTA-CATENIN AND ARVCF 著者: LAURA, R.P. / WITT, A.S. / HELD, H.A. / GERSTNER, R. / DESHAYES, K. / KOEHLER, M.F. / KOSIK, K.S. / SIDHU, S.S. / LASKY, L.A. #3: ジャーナル: J.Biol.Chem. / 年: 2001 タイトル: ERBIN IS A PROTEIN CONCENTRATED AT POSTSYNAPTIC MEMBRANES THAT INTERACTS WITH PSD-95 著者: HUANG, Y.Z. / WANG, Q. / XIONG, W.C. / MEI, L. #4: ジャーナル: J.Biol.Chem. / 年: 2001 タイトル: THE ERBB2/HER2 RECEPTOR DIFFERENTIALLY INTERACTS WITH ERBIN AND PICK1 PSD-95/DLG/ZO-1 DOMAIN PROTEINS 著者: JAULIN-BASTARD, F. / SAITO, H. / LEBIVIC, A. / OLLENDORFF, V. / MARCHETTO, S. / BIRNBAUM, D. / BORG, J.P. | ||||||
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 | 1mfg.cif.gz | 59.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1mfg.ent.gz | 43.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1mfg.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/mf/1mfg ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mfg | 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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詳細 | COORDINATES REPRESENT THE COMPLETE BIOLOGICAL ASSEMBLY |
-要素
#1: タンパク質 | 分子量: 10292.593 Da / 分子数: 1 / 断片: PDZ DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PGEX-KT / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q96RT1 |
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#2: タンパク質・ペプチド | 分子量: 1004.134 Da / 分子数: 1 / 断片: PEPTIDE EYLGLDVPV / 由来タイプ: 合成 / 詳細: PEPTIDE SYNTHESIZED CHEMICALLY / 参照: UniProt: P04626*PLUS |
#3: 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: 1.71 Å3/Da / 溶媒含有率: 39.16 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4.6 詳細: 12-15%PEG 4000, 100mM Ammonium Acetate, 100mM Sodium Acetate, 10% Glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 20 ℃ / pH: 8.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: CHESS / ビームライン: F2 / 波長: 0.97861 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2002年3月10日 / 詳細: DUAL SLITS |
放射 | モノクロメーター: SAGITALLY FOCUSED Si(111) / 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 | 波長: 0.97861 Å / 相対比: 1 |
反射 | 解像度: 1.25→25 Å / Num. all: 24313 / Num. obs: 24313 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
反射 シェル | 解像度: 1.25→1.29 Å / % possible all: 91.4 |
反射 | *PLUS % possible obs: 92.7 % / Rmerge(I) obs: 0.025 |
反射 シェル | *PLUS % possible obs: 91.4 % / Rmerge(I) obs: 0.037 / Mean I/σ(I) obs: 16.8 |
-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: 1.25→25 Å / Num. parameters: 8637 / Num. restraintsaints: 10570 / 交差検証法: FREE R / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.6% Water molecules 131, 132 and 133 occupy the site where the disordered component of HIS1347 with alternate conformer B is modeled.
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 766 / Occupancy sum non hydrogen: 929.08 | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.25→25 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: SHELXL / バージョン: 97 / 分類: refinement | |||||||||||||||||||||||||||||||||
精密化 | *PLUS 最低解像度: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.128 | |||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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