+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3dwy | ||||||
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タイトル | Crystal Structure of the Bromodomain of Human CREBBP | ||||||
要素 | CREB-binding protein | ||||||
キーワード | TRANSFERASE / bromodomain / CREB binding protein / structural genomics consortium / SGC / Activator / Disease mutation / Host-virus interaction / Metal-binding / Methylation / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Zinc-finger | ||||||
機能・相同性 | 機能・相同性情報 peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / embryonic digit morphogenesis / homeostatic process / protein acetylation / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Transcriptional and post-translational regulation of MITF-M expression and activity / Attenuation phase / cellular response to nutrient levels / canonical NF-kappaB signal transduction / regulation of cellular response to heat / histone acetyltransferase activity / histone acetyltransferase / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / transcription coactivator binding / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription corepressor activity / cellular response to UV / p53 binding / Circadian Clock / rhythmic process / TRAF3-dependent IRF activation pathway / HATs acetylate histones / protein-containing complex assembly / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / damaged DNA binding / transcription coactivator activity / response to hypoxia / nuclear body / chromatin binding / regulation of DNA-templated transcription / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm 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: 1.98 Å | ||||||
データ登録者 | Filippakopoulos, P. / Picaud, S. / Fedorov, O. / Karim, R. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. / Bountra, C. ...Filippakopoulos, P. / Picaud, S. / Fedorov, O. / Karim, R. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
引用 | ジャーナル: Cell(Cambridge,Mass.) / 年: 2012 タイトル: Histone recognition and large-scale structural analysis of the human bromodomain family. 著者: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S. | ||||||
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 | 3dwy.cif.gz | 64.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3dwy.ent.gz | 47.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3dwy.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/dw/3dwy ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dwy | HTTPS FTP |
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-関連構造データ
関連構造データ | 2nxbSC 2oo1SC 2ossSC 2ouoSC 2rfjSC 3d7cC 3daiSC 3gg3C 3hmeC 3hmfC 3hmhC 3i3jC 3iu5C 3iu6C 3lxjC 3mb3C 3mb4C 3mqmC 3nxbC 3p1cC 3p1dC 3q2eC 3rcwC 3tlpC 3uv2C 3uv4C 3uv5C 3uvdC 3uvwC 3uvxC 3uvyC 3uw9C 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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2 |
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単位格子 |
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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Ens-ID: 1
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-要素
#1: タンパク質 | 分子量: 14223.349 Da / 分子数: 2 / 断片: Bromo domain: residues 1084-1197 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CREBBP, CBP / プラスミド: pNIC28-Bsa4 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)-R3 / 参照: UniProt: Q92793, histone acetyltransferase #2: 化合物 | #3: 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: 2.02 Å3/Da / 溶媒含有率: 38.98 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 詳細: 0.2M KSCN, 25% PEG3350, 5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU FR-E SUPERBRIGHT / 波長: 1.5 Å |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2008年6月19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: 1.5 Å / 相対比: 1 |
反射 | 解像度: 1.98→23.65 Å / Num. obs: 15467 / % possible obs: 99.9 % / 冗長度: 3.7 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 11.6 |
反射 シェル | 解像度: 1.98→2.09 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2 / Num. unique all: 2257 / Rsym value: 0.086 / % possible all: 100 |
-位相決定
位相決定 | 手法: 分子置換 | |||||||||
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Phasing MR | Rfactor: 50.13 / Model details: Phaser MODE: MR_AUTO
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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: ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI 解像度: 1.98→23.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU B: 8.047 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.165 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 81.41 Å2 / Biso mean: 30.488 Å2 / Biso min: 6.83 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.98→23.65 Å
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拘束条件 |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS精密化 シェル | 解像度: 1.98→2.031 Å / Total num. of bins used: 20
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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