+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3ml6 | ||||||
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タイトル | a complex between Dishevelled2 and clathrin adaptor AP-2 | ||||||
要素 | Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu | ||||||
キーワード | PROTEIN TRANSPORT / Dishevelled (Dishevelled) / AP2 / Frizzled internalization / non-canonical Wnt signaling | ||||||
機能・相同性 | 機能・相同性情報 WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Signaling by Hippo / Disassembly of the destruction complex and recruitment of AXIN to the membrane / segmentation / planar cell polarity pathway involved in neural tube closure / Gap junction degradation / Formation of annular gap junctions ...WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / convergent extension involved in neural plate elongation / Signaling by Hippo / Disassembly of the destruction complex and recruitment of AXIN to the membrane / segmentation / planar cell polarity pathway involved in neural tube closure / Gap junction degradation / Formation of annular gap junctions / Asymmetric localization of PCP proteins / cochlea morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Degradation of DVL / segment specification / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / regulation of vesicle size / RHO GTPases Activate Formins / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / frizzled binding / aggresome / negative regulation of protein localization to plasma membrane / Wnt signaling pathway, planar cell polarity pathway / クラスリン / low-density lipoprotein particle receptor binding / heart looping / outflow tract morphogenesis / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / canonical Wnt signaling pathway / lateral plasma membrane / heart morphogenesis / クラスリン / positive regulation of JUN kinase activity / neural tube closure / positive regulation of JNK cascade / intracellular protein transport / protein localization / terminal bouton / receptor internalization / Wntシグナル経路 / small GTPase binding / positive regulation of GTPase activity / : / disordered domain specific binding / protein-macromolecule adaptor activity / apical part of cell / regulation of cell population proliferation / 細胞皮質 / heart development / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / transmembrane transporter binding / 細胞骨格 / nuclear body / intracellular signal transduction / positive regulation of protein phosphorylation / protein domain specific binding / シナプス / glutamatergic synapse / lipid binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of transcription by RNA polymerase II / 核質 / identical protein binding / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) Rattus norvegicus (ドブネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å | ||||||
データ登録者 | Yu, A. / Xing, Y. / Harrison, S.C. / Kirchhausen, T.L. | ||||||
引用 | ジャーナル: Structure / 年: 2010 タイトル: Structural analysis of the interaction between Dishevelled2 and clathrin AP-2 adaptor, a critical step in noncanonical Wnt signaling. 著者: Yu, A. / Xing, Y. / Harrison, S.C. / Kirchhausen, T. | ||||||
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 | 3ml6.cif.gz | 402.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3ml6.ent.gz | 328.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3ml6.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/ml/3ml6 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3ml6 | 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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単位格子 |
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詳細 | none |
-要素
#1: タンパク質 | 分子量: 43403.367 Da / 分子数: 6 断片: PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435) 由来タイプ: 組換発現 由来: (組換発現) Mus musculus (ハツカネズミ), (組換発現) Rattus norvegicus (ドブネズミ) 遺伝子: Dishevlled2, u2 / プラスミド: pPROEX-HTC / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: Q60838, UniProt: P84092 配列の詳細 | THE STRUCTURE IS REPRESENTATIVE OF A CHIMERIC PROTEIN BETWEEN DISHEVLLED2 AND CLATHRIN ADAPTOR AP-2 ...THE STRUCTURE IS REPRESENTA | |
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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: 4 Å3/Da / 溶媒含有率: 69.27 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 詳細: 0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: APS / ビームライン: 24-ID-E / 波長: 0.98 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD |
放射 | モノクロメーター: Si 111 CHANNEL / 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: 0.98 Å / 相対比: 1 |
反射 | 解像度: 3.5→100 Å / Num. all: 51791 / Num. obs: 51429 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / 冗長度: 3.6 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 11.3 |
反射 シェル | 解像度: 3.5→3.56 Å / 冗長度: 3.5 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2485 / Rsym value: 0.774 / % possible all: 97 |
-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: 1BW8, 1FSH 解像度: 3.5→49.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5714272.84 / Data cutoff low absF: 0 / 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: 66.0607 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 117.5 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: 3.5→49.07 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3.5→3.72 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |