+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1vkx | ||||||
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タイトル | CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA | ||||||
要素 |
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キーワード | TRANSCRIPTION/DNA / TRANSCRIPTION FACTOR (転写因子) / NF-KB (NF-κB) / HETERODIMER / DNA-BINDING / TRANSCRIPTION-DNA COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process ...cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / antibacterial innate immune response / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to peptide / acetaldehyde metabolic process / cellular response to interleukin-17 / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / negative regulation of interleukin-12 production / ankyrin repeat binding / negative regulation of protein sumoylation / cellular response to dsRNA / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / NF-kappaB complex / cellular response to angiotensin / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / cellular response to organic cyclic compound / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of transcription initiation by RNA polymerase II / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / lymph node development / cellular response to interleukin-1 / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / heat shock protein binding / response to muscle stretch / Neutrophil degranulation / positive regulation of interleukin-12 production / response to interleukin-1 / negative regulation of angiogenesis / protein sequestering activity / negative regulation of miRNA transcription / liver development / response to progesterone / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / response to bacterium / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / B cell receptor signaling pathway / protein catabolic process / response to insulin / defense response 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / MOLECULAR REPLACEMEN / 解像度: 2.9 Å | ||||||
データ登録者 | Chen, F. / Huang, D.B. / Ghosh, G. | ||||||
引用 | ジャーナル: Nature / 年: 1998 タイトル: Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. 著者: Chen, F.E. / Huang, D.B. / Chen, Y.Q. / Ghosh, G. #1: ジャーナル: Nature / 年: 1995 タイトル: Structure of NF-Kb p50 Homodimer Bound to a Kb Site 著者: Ghosh, G. / Duyne, G.V. / Ghosh, S. / Sigler, P.B. | ||||||
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 | 1vkx.cif.gz | 141.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1vkx.ent.gz | 107 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1vkx.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/vk/1vkx ftp://data.pdbj.org/pub/pdb/validation_reports/vk/1vkx | 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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-要素
#1: DNA鎖 | 分子量: 3669.389 Da / 分子数: 1 / 由来タイプ: 合成 詳細: ACTIVE NF-KAPPA-B IS A HETERODIMER OF AN ABOUT 50 KD DNA-BINDING SUBUNIT AND THE WEAK DNA-BINDING SUBUNIT P65 |
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#2: DNA鎖 | 分子量: 3656.407 Da / 分子数: 1 / 由来タイプ: 合成 詳細: ACTIVE NF-KAPPA-B IS A HETERODIMER OF AN ABOUT 50 KD DNA-BINDING SUBUNIT AND THE WEAK DNA-BINDING SUBUNIT P65 |
#3: タンパク質 | 分子量: 30984.045 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q04207 |
#4: タンパク質 | 分子量: 34924.871 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: P25799 |
-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: 3.99 Å3/Da / 溶媒含有率: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 / 詳細: pH 5.50, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 |
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結晶化 | *PLUS 温度: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 105 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU / 波長: 1.5418 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1997年4月1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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.9→30 Å / Num. obs: 26430 / % possible obs: 97 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.8 |
反射 シェル | 解像度: 2.9→3 Å / Rmerge(I) obs: 0.45 / % possible all: 88 |
反射 | *PLUS Num. measured all: 88449 |
反射 シェル | *PLUS % possible obs: 88 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: MOLECULAR REPLACEMEN 開始モデル: ONE MONOMER OF P50/DNA COMPLEX AND ONE MONO OF P65/DNA COMPLEX 解像度: 2.9→8 Å / σ(F): 2
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精密化ステップ | サイクル: LAST / 解像度: 2.9→8 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: X-PLOR / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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