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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1zq3 | ||||||
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タイトル | NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC | ||||||
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![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / HELIX-TURN-HELIX / HOMEODOMAIN / DNA-BINDING DOMAIN / K50 / RECOGNITION HELIX / TRANSCRIPTION FACTOR / TRANSLATIONAL CONTROL / TRANSCRIPTION-DNA COMPLEX | ||||||
機能・相同性 | ![]() anterior region determination / maternal determination of anterior/posterior axis, embryo / torso signaling pathway / segment polarity determination / anterior/posterior axis specification, embryo / anterior/posterior axis specification / oogenesis / translation repressor activity / mRNA 3'-UTR binding / negative regulation of translation ...anterior region determination / maternal determination of anterior/posterior axis, embryo / torso signaling pathway / segment polarity determination / anterior/posterior axis specification, embryo / anterior/posterior axis specification / oogenesis / translation repressor activity / mRNA 3'-UTR binding / negative regulation of translation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | 溶液NMR / protein structure - fast torsion angle dynamics algorithm (CYANA2.0), DNA structure - NUCGEN, simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex - simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex refinement - explicit solvent MD simulations (AMBER7.0) | ||||||
![]() | Baird-Titus, J.M. / Rance, M. / Clark-Baldwin, K. / Ma, J. / Vrushank, D. | ||||||
![]() | ![]() タイトル: The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. 著者: Baird-Titus, J.M. / Clark-Baldwin, K. / Dave, V. / Caperelli, C.A. / Ma, J. / Rance, M. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
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PDB形式 | ![]() | 639 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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NMR アンサンブル |
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要素
#1: DNA鎖 | 分子量: 3887.537 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: CONSENSUS DNA BINDING SITE SENSE STRAND |
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#2: DNA鎖 | 分子量: 4056.646 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: CONSENSUS DNA BINDING SITE ANTI-SENSE STRAND |
#3: タンパク質 | 分子量: 7963.067 Da / 分子数: 1 / Fragment: Homeodomain (residues 97-163) / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: bcd / プラスミド: pET41a-Novagen / 発現宿主: ![]() ![]() |
-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||
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NMR実験 |
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試料調製
詳細 | 内容: 1mM Bicoid Homeodomain (15N/13C), 1mM Duplex DNA (unlabeled), 10mM phosphate buffer, pH 7.0, 1mM DTT, 1mM PMSF, 1mM EDTA, 1mM sodium azide, 0.3mM leupeptin, 0.2mM pefabloc (Roche), 90% H2O, 10% D2O 溶媒系: 90% H2O/10% D2O |
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試料状態 | pH: 7 / 圧: 1 atm / 温度: 295 K |
-NMR測定
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M | |||||||||||||||
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放射波長 | 相対比: 1 | |||||||||||||||
NMRスペクトロメーター |
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解析
NMR software |
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精密化 | 手法: protein structure - fast torsion angle dynamics algorithm (CYANA2.0), DNA structure - NUCGEN, simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex - ...手法: protein structure - fast torsion angle dynamics algorithm (CYANA2.0), DNA structure - NUCGEN, simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex - simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex refinement - explicit solvent MD simulations (AMBER7.0) ソフトェア番号: 1 詳細: 1724 total restraints used, 1076 protein distance restraints(NOESY), 34 protein hydrogen bond restraints(3D NOESY ,i-i+4), 134 angle restraints(HNHA), 192 DNA distance restraints(2D NOESY), ...詳細: 1724 total restraints used, 1076 protein distance restraints(NOESY), 34 protein hydrogen bond restraints(3D NOESY ,i-i+4), 134 angle restraints(HNHA), 192 DNA distance restraints(2D NOESY), 55 watson-crick restraints(B-DNA), 200 DNA angle restraints(B-DNA), 33 protein-DNA distance restraints (2D NOESY) | ||||||||||||||||||||
代表構造 | 選択基準: closest to the average | ||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 20 |