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基本情報
登録情報 | データベース: PDB / ID: 3mi9 | ||||||
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タイトル | Crystal structure of HIV-1 Tat complexed with human P-TEFb | ||||||
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![]() | PROTEIN BINDING / P-TEFb / Tat / HIV-1 | ||||||
機能・相同性 | ![]() trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin ...trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / nucleus localization / evasion of host immune response / molecular sequestering activity / host cell nucleolus / actinin binding / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / positive regulation of DNA-templated transcription, elongation / RNA polymerase binding / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / transcription elongation-coupled chromatin remodeling / regulation of cyclin-dependent protein serine/threonine kinase activity / replication fork processing / negative regulation of peptidyl-threonine phosphorylation / cellular response to cytokine stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / RNA-binding transcription regulator activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / regulation of DNA repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / molecular condensate scaffold activity / transcription elongation factor complex / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PKR-mediated signaling / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell population proliferation / host cell cytoplasm / transcription by RNA polymerase II / transcription cis-regulatory region binding / regulation of cell cycle / protein kinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / virus-mediated perturbation of host defense response / protein serine/threonine kinase activity / DNA-templated transcription / chromatin binding / host cell nucleus / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Tahirov, T.H. / Babayeva, N.D. / Varzavand, K. / Cooper, J.J. / Sedore, S.C. / Price, D.H. | ||||||
![]() | ![]() タイトル: Crystal structure of HIV-1 Tat complexed with human P-TEFb. 著者: Tahirov, T.H. / Babayeva, N.D. / Varzavand, K. / Cooper, J.J. / Sedore, S.C. / Price, D.H. | ||||||
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
PDBx/mmCIF形式 | ![]() | 148.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 113.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 456.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 475 KB | 表示 | |
XML形式データ | ![]() | 29.1 KB | 表示 | |
CIF形式データ | ![]() | 41.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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リンク
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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: 40692.152 Da / 分子数: 1 / 断片: UNP residues 1-345, Protein kinase domain / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 株 (発現宿主): SF9 参照: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase | ||
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#2: タンパク質 | 分子量: 30877.320 Da / 分子数: 1 / 断片: UNP residues 1-266 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 株 (発現宿主): SF9 / 参照: UniProt: O60563 | ||
#3: タンパク質 | 分子量: 9848.327 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 株: isolate HXB2 group M subtype B / 遺伝子: tat / プラスミド: pENTR/SD/D-TOPO vector (Invitrogen K2420) / 細胞株 (発現宿主): BL21 insect cells 発現宿主: ![]() ![]() 株 (発現宿主): SF9 / 参照: UniProt: P04608 | ||
#4: 化合物 | #5: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.96 Å3/Da / 溶媒含有率: 58.43 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 詳細: 50 mM HEPES buffer (pH 7.5), 4.25-5% PEG 20,000, 1 mM TCEP, and 20 mM glycyl-glycyl-glycine , VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
-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: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2009年10月17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: 2.1→40 Å / Num. obs: 51839 / % possible obs: 90.9 % / Observed criterion σ(F): -2 / 冗長度: 2.5 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 35 |
反射 シェル | 解像度: 2.1→2.14 Å / 冗長度: 2.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2531 / % possible all: 89 |
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解析
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 3blh 解像度: 2.1→30.63 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2384386.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 58.0275 Å2 / ksol: 0.36834 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 46.7 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: 2.1→30.63 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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