+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1le9 | ||||||
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タイトル | Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti | ||||||
要素 |
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キーワード | TRANSCRIPTION/DNA / transcription factor (転写因子) / NF-kB-DNA complex / 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 / Downstream TCR signaling / prolactin signaling pathway / cellular response to interleukin-17 / 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 / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / 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 / hair follicle development / NF-kappaB binding / 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 / negative regulation of insulin receptor signaling pathway / response to cAMP / cellular response to brain-derived neurotrophic factor stimulus / tumor necrosis factor-mediated signaling pathway / heat shock protein binding / response to muscle stretch / Neutrophil degranulation / positive regulation of interleukin-12 production / negative regulation of angiogenesis / response to interleukin-1 / 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 / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / response to bacterium / B cell receptor signaling pathway / protein catabolic process / response to insulin / transcription coactivator binding 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 / 分子置換 / 解像度: 3 Å | ||||||
データ登録者 | Benjamin, B. / Huang, D.B. / Chen-Park, F.E. / Sigler, P.B. / Ghosh, G. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2002 タイトル: The x-ray crystal structure of the NF-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B site. 著者: Berkowitz, B. / Huang, D.B. / Chen-Park, F.E. / Sigler, P.B. / Ghosh, G. | ||||||
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 | 1le9.cif.gz | 264.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1le9.ent.gz | 209.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1le9.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/le/1le9 ftp://data.pdbj.org/pub/pdb/validation_reports/le/1le9 | 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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2 |
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単位格子 |
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-要素
#1: DNA鎖 | 分子量: 3644.376 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: Ig/HIV2-kB DNA #2: DNA鎖 | 分子量: 3680.432 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: Ig/HIV2-kB DNA #3: タンパク質 | 分子量: 31115.236 Da / 分子数: 2 / Fragment: p65 RHR / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: rela / プラスミド: pET29b / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q04207 #4: タンパク質 | 分子量: 35056.066 Da / 分子数: 2 / Fragment: p50 RHR / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: nfkb1 / プラスミド: pET29b / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P25799 |
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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: 2.88 Å3/Da / 溶媒含有率: 57.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 110 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 Å |
検出器 | タイプ: MARRESEARCH / 検出器: AREA DETECTOR / 日付: 1999年9月2日 |
放射 | モノクロメーター: mirrors / 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: 3→30 Å / Num. obs: 33446 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 7.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.1 |
反射 シェル | 解像度: 3→3.1 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 98 |
反射 | *PLUS % possible obs: 99 % / Num. measured all: 249074 |
反射 シェル | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.434 |
-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: PDB ENTRY 1VKX 解像度: 3→30 Å / Isotropic thermal model: Isotropic / σ(F): 2 / 立体化学のターゲット値: Engh & Huber
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精密化ステップ | サイクル: LAST / 解像度: 3→30 Å
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拘束条件 |
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精密化 | *PLUS 最低解像度: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS |