+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1my5 | ||||||
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タイトル | NF-kappaB p65 subunit dimerization domain homodimer | ||||||
要素 | NF-kappaB p65 (RelA) subunit | ||||||
キーワード | TRANSCRIPTION (転写 (生物学)) / Immunoglobulin (抗体) / Ig / beta-sandwich / beta-sheet (Βシート) / homodimer / DNA-binding / Transcription regulation / Activator / Nuclear protein / Phosphorylation (リン酸化) | ||||||
機能・相同性 | 機能・相同性情報 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 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation ...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 / TRAF6 mediated NF-kB activation / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / 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 / ankyrin repeat binding / negative regulation of protein sumoylation / 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 / 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 lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / 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 / cellular response to interleukin-1 / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / response to interleukin-1 / negative regulation of angiogenesis / 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 / peptide binding / response to bacterium / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / protein catabolic process / response to insulin / defense response / transcription coactivator binding / negative regulation of protein catabolic process / chromatin DNA binding / cellular response to hydrogen peroxide / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / histone deacetylase binding / chromatin organization / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region 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: 1.8 Å | ||||||
Model details | transcription factor p65 | ||||||
データ登録者 | Huxford, T. / Mishler, D. / Phelps, C.B. / Huang, D.-B. / Sengchanthalangsy, L.L. / Reeves, R. / Hughes, C.A. / Komives, E.A. / Ghosh, G. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2002 タイトル: Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/I kappaB alpha complex formation 著者: Huxford, T. / Mishler, D. / Phelps, C.B. / Huang, D.-B. / Sengchanthalangsy, L.L. / Reeves, R. / Hughes, C.A. / Komives, E.A. / 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 | 1my5.cif.gz | 55.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1my5.ent.gz | 41.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1my5.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/my/1my5 ftp://data.pdbj.org/pub/pdb/validation_reports/my/1my5 | 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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 13201.880 Da / 分子数: 2 / 断片: residues 191-304 (dimerization domain) / 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: pET11a / 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 #2: 水 | ChemComp-HOH / | |
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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: 2.18 Å3/Da / 溶媒含有率: 43.47 % | ||||||||||||||||||||||||||||||
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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: 7.5 詳細: 0.1M sodium HEPES, 0.2M sodium tartrate, 2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 18 ℃ / 手法: 蒸気拡散法 | ||||||||||||||||||||||||||||||
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 / 波長: 1.5418 Å |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2001年10月22日 / 詳細: Osmic optics |
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: 1.8→30 Å / Num. all: 21911 / Num. obs: 20531 / % possible obs: 93.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / 冗長度: 5.6 % / Rsym value: 0.053 / Net I/σ(I): 21.9 |
反射 シェル | 解像度: 1.8→1.86 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3 / % possible all: 58 |
反射 | *PLUS Num. measured all: 114510 / Rmerge(I) obs: 0.053 |
反射 シェル | *PLUS % possible obs: 58 % |
-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 id 1bft 解像度: 1.8→30 Å / 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: 1.8→30 Å
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拘束条件 |
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精密化 | *PLUS 最低解像度: 30 Å / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS |