+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5bt2 | |||||||||
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タイトル | MeCP2 MBD domain (A140V) in complex with methylated DNA | |||||||||
要素 |
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キーワード | DNA BINDING PROTEIN/DNA / A/T run / MeCP2 (MECP2) / hydration spine / methylated DNA / DNA BINDING PROTEIN-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / : ...trans-synaptic signaling by BDNF / regulation of action potential firing threshold / negative regulation of respiratory gaseous exchange / Loss of MECP2 binding ability to 5hmC-DNA / cellular response to isoquinoline alkaloid / positive regulation of anterograde dense core granule transport / positive regulation of retrograde dense core granule transport / positive regulation of branching morphogenesis of a nerve / catecholamine secretion / : / MECP2 regulates transcription of genes involved in GABA signaling / biogenic amine metabolic process / negative regulation of dendrite extension / principal sensory nucleus of trigeminal nerve development / cardiolipin metabolic process / negative regulation of locomotion involved in locomotory behavior / Loss of MECP2 binding ability to 5mC-DNA / nervous system process involved in regulation of systemic arterial blood pressure / 深部感覚 / : / negative regulation of primary miRNA processing / negative regulation of smooth muscle cell differentiation / MECP2 regulates transcription of neuronal ligands / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of dendritic spine development / Transcriptional Regulation by MECP2 / regulation of respiratory gaseous exchange by nervous system process / double-stranded methylated DNA binding / inositol metabolic process / ゲノム刷り込み / thalamus development / positive regulation of microtubule nucleation / glucocorticoid metabolic process / ventricular system development / cellular response to potassium ion / unmethylated CpG binding / phosphatidylcholine metabolic process / positive regulation of synaptic plasticity / respiratory gaseous exchange by respiratory system / oligodendrocyte development / olfactory bulb development / striatum development / positive regulation of dendrite extension / response to other organism / siRNA binding / neuron maturation / methyl-CpG binding / MECP2 regulates transcription factors / Loss of phosphorylation of MECP2 at T308 / response to ionizing radiation / spinal cord development / positive regulation of dendritic spine development / regulation of synapse organization / lung alveolus development / glutamine metabolic process / startle response / dendrite development / social behavior / negative regulation of blood vessel endothelial cell migration / Regulation of MECP2 expression and activity / negative regulation of astrocyte differentiation / behavioral fear response / glial cell proliferation / Nuclear events stimulated by ALK signaling in cancer / ヘテロクロマチン / long-term memory / heterochromatin formation / four-way junction DNA binding / MECP2 regulates neuronal receptors and channels / positive regulation of glial cell proliferation / Notchシグナリング / sensory perception of pain / synapse assembly / histone reader activity / excitatory postsynaptic potential / negative regulation of angiogenesis / adult locomotory behavior / cerebellum development / post-embryonic development / response to cocaine / molecular condensate scaffold activity / promoter-specific chromatin binding / long-term synaptic potentiation / hippocampus development / response to lead ion / visual learning / protein localization / chromatin DNA binding / cerebral cortex development / histone deacetylase binding / transcription corepressor activity / response to estradiol / heart development / 遺伝子発現 / postsynapse / negative regulation of neuron apoptotic process / nucleic acid binding / molecular adaptor activity / response to hypoxia / protein domain specific binding 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: 2.2 Å | |||||||||
データ登録者 | Ho, K.L. / Chia, J.Y. / Tan, W.S. / Ng, C.L. / Hu, N.J. / Foo, H.L. | |||||||||
資金援助 | マレーシア, 2件
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引用 | ジャーナル: Sci Rep / 年: 2016 タイトル: A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence. 著者: Chia, J.Y. / Tan, W.S. / Ng, C.L. / Hu, N.J. / Foo, H.L. / Ho, K.L. | |||||||||
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 | 5bt2.cif.gz | 93.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5bt2.ent.gz | 67.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5bt2.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/bt/5bt2 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/5bt2 | HTTPS FTP |
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-関連構造データ
関連構造データ | 3c2iS S: 精密化の開始モデル |
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類似構造データ |
-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
#1: タンパク質 | 分子量: 11155.526 Da / 分子数: 1 / 断片: MBD domain, UNP residues 77-167 / 変異: A140V / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MECP2 / プラスミド: pET30b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)pLys / 参照: UniProt: P51608 |
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#2: DNA鎖 | 分子量: 6138.003 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) |
#3: DNA鎖 | 分子量: 6156.032 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) |
#4: 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: 2.18 Å3/Da / 溶媒含有率: 43.49 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 30% PEG 2000, 200 mM ammonium acetate, 10 mM magnesium acetate, 50 mM sodium cacodylate PH範囲: 6.0-6.7 |
-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: Diamond / ビームライン: I02 / 波長: 0.9795 Å |
検出器 | タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2012年12月21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: 0.9795 Å / 相対比: 1 |
反射 | 解像度: 2.2→48.5 Å / Num. obs: 10482 / % possible obs: 98.9 % / 冗長度: 3.8 % / Net I/σ(I): 9.2 |
-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: 3C2I 解像度: 2.2→48.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 13.84 / SU ML: 0.179 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.198 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 132.62 Å2 / Biso mean: 73.464 Å2 / Biso min: 39.01 Å2
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精密化ステップ | サイクル: final / 解像度: 2.2→48.5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.182→2.239 Å / Total num. of bins used: 20
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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