+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7nqp | |||||||||
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タイトル | 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound LvD1009 | |||||||||
要素 |
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キーワード | PEPTIDE BINDING PROTEIN / benzaldehyde (ベンズアルデヒド) / covalent fragment / p65 / 1433 | |||||||||
機能・相同性 | 機能・相同性情報 acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 ...acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / Interleukin-1 processing / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / NF-kappaB complex / response to UV-B / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of miRNA metabolic process / regulation of epidermal cell division / response to cobalamin / protein kinase C inhibitor activity / positive regulation of T cell receptor signaling pathway / positive regulation of epidermal cell differentiation / keratinocyte development / ケラチン / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / phosphoserine residue binding / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / establishment of skin barrier / cellular response to interleukin-1 / response to amino acid / cellular defense response / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Purinergic signaling in leishmaniasis infection / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / response to cAMP / tumor necrosis factor-mediated signaling pathway / protein kinase A signaling / response to muscle stretch / protein export from nucleus / negative regulation of innate immune response / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / protein sequestering activity / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / : / positive regulation of protein export from nucleus / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to progesterone / response to cytokine / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / response to ischemia / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Activation of NF-kappaB in B cells / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.24 Å | |||||||||
データ登録者 | Wolter, M. / Dijck, L.v. / Cossar, P.J. / Ottmann, C. | |||||||||
資金援助 | 2件
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引用 | ジャーナル: J.Am.Chem.Soc. / 年: 2021 タイトル: Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions. 著者: Cossar, P.J. / Wolter, M. / van Dijck, L. / Valenti, D. / Levy, L.M. / Ottmann, C. / Brunsveld, L. | |||||||||
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 | 7nqp.cif.gz | 72 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7nqp.ent.gz | 50.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7nqp.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/nq/7nqp ftp://data.pdbj.org/pub/pdb/validation_reports/nq/7nqp | HTTPS FTP |
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-関連構造データ
関連構造データ | 7aogC 7axnC 7ayfC 7az1C 7az2C 7bdpC 7bdtC 7bdyC 7bfwC 7bg3C 7bgqC 7bgrC 7bgvC 7bgwC 7nifC 7nigC 7nixC 7nj6C 7nj8C 7njaC 7nrkC 7nrlC 7nsvC 6qhlS S: 精密化の開始モデル C: 同じ文献を引用 (文献) |
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類似構造データ |
-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: タンパク質 | 分子量: 28226.518 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SFN, HME1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P31947 |
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#2: タンパク質・ペプチド | 分子量: 1412.429 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: alternative sequencing (E49R) with ID CAA80524 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q04206 |
#3: 化合物 | ChemComp-TJ8 / |
#4: 化合物 | ChemComp-MG / |
#5: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | Y |
-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: 2.44 Å3/Da / 溶媒含有率: 49.54 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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放射光源 | 由来: シンクロトロン / サイト: PETRA III, DESY / ビームライン: P11 / 波長: 1.0332 Å | ||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2020年5月12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: 1.0332 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 1.24→66.38 Å / Num. obs: 81921 / % possible obs: 99.8 % / 冗長度: 12 % / Biso Wilson estimate: 14.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.03 / Rrim(I) all: 0.106 / Net I/σ(I): 11.1 / Num. measured all: 985833 / Scaling rejects: 1632 | ||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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-位相決定
位相決定 | 手法: 分子置換 |
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-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: 6QHL 解像度: 1.24→66.38 Å / SU ML: 0.15 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.41 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 65.17 Å2 / Biso mean: 20.4706 Å2 / Biso min: 9.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.24→66.38 Å
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29
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