+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6yp2 | |||||||||
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タイトル | 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-011 | |||||||||
要素 |
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キーワード | PEPTIDE BINDING PROTEIN / 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 / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / Interleukin-1 processing / 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 / Regulation of NFE2L2 gene expression / 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 / regulation of epidermal cell division / protein kinase C inhibitor activity / 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 / hair follicle development / NF-kappaB binding / 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 / response to amino acid / establishment of skin barrier / cellular response to interleukin-1 / 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 / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / protein export from nucleus / negative regulation of innate immune response / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / negative regulation of angiogenesis / response to interleukin-1 / protein sequestering activity / 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 / response to progesterone / response to organic substance / positive regulation of interleukin-1 beta production / stem cell proliferation / response to cytokine / response to ischemia / Translocation of SLC2A4 (GLUT4) to the plasma membrane / 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 / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / 分子置換 / 解像度: 1.8 Å | |||||||||
データ登録者 | Wolter, M. / Ottmann, C. | |||||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: Angew.Chem.Int.Ed.Engl. / 年: 2020 タイトル: Fragment-Based Stabilizers of Protein-Protein Interactions through Imine-Based Tethering. 著者: Wolter, M. / Valenti, D. / Cossar, P.J. / Levy, L.M. / Hristeva, S. / Genski, T. / Hoffmann, T. / Brunsveld, L. / Tzalis, D. / Ottmann, C. | |||||||||
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 | 6yp2.cif.gz | 73 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6yp2.ent.gz | 51.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6yp2.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/yp/6yp2 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6yp2 | 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: タンパク質 | 分子量: 26558.914 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 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q04206*PLUS |
#3: 化合物 | ChemComp-CL / |
#4: 化合物 | ChemComp-P5N / |
#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: 2.59 Å3/Da / 溶媒含有率: 52.44 % |
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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: SEALED TUBE / タイプ: RIGAKU MICROMAX-003 / 波長: 1.54187 Å | ||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS PILATUS 200K / 検出器: PIXEL / 日付: 2018年10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: 1.54187 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 1.8→41.77 Å / Num. obs: 26657 / % possible obs: 98.1 % / 冗長度: 3.1 % / Biso Wilson estimate: 11.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Net I/σ(I): 13.9 | ||||||||||||||||||||||||||||||
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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Phasing MR | R rigid body: 0.372
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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: 1.8→41.769 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.49 / 位相誤差: 21.18
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 88.75 Å2 / Biso mean: 15.9511 Å2 / Biso min: 0.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.8→41.769 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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