+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 6ler | ||||||
---|---|---|---|---|---|---|---|
タイトル | 169 bp nucleosome harboring non-identical cohesive DNA termini. | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN / Nucleosome / DNA-protein complex / DNA BINDING PROTEIN-DNA complex / Linker Histone / H1.0 | ||||||
機能・相同性 | ![]() negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() other sequences (unknown) | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Sharma, D. / Adhireksan, Z. / Lee, P.L. / Davey, C.A. | ||||||
資金援助 | ![]()
| ||||||
![]() | ![]() タイトル: Engineering nucleosomes for generating diverse chromatin assemblies. 著者: Adhireksan, Z. / Sharma, D. / Lee, P.L. / Bao, Q. / Padavattan, S. / Shum, W.K. / Davey, G.E. / Davey, C.A. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 642.9 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 520.4 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 573.6 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 608.2 KB | 表示 | |
XML形式データ | ![]() | 67.6 KB | 表示 | |
CIF形式データ | ![]() | 97.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
単位格子 |
|
-
要素
-タンパク質 , 4種, 16分子 KOAELPBFMQCGNRDH
#1: タンパク質 | 分子量: 15437.167 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 遺伝子: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ 発現宿主: ![]() ![]() #2: タンパク質 | 分子量: 11394.426 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 遺伝子: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, ...遺伝子: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 発現宿主: ![]() ![]() #3: タンパク質 | 分子量: 14165.551 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #4: タンパク質 | 分子量: 13935.239 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
---|
-DNA鎖 , 2種, 4分子 SJTI
#5: DNA鎖 | 分子量: 52330.262 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) other sequences (unknown) / 発現宿主: ![]() ![]() #6: DNA鎖 | 分子量: 52008.266 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) other sequences (unknown) / 発現宿主: ![]() ![]() |
---|
-非ポリマー , 3種, 42分子 




#7: 化合物 | ChemComp-CA / #8: 化合物 | #9: 水 | ChemComp-HOH / | |
---|
-詳細
研究の焦点であるリガンドがあるか | N |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.71 Å3/Da / 溶媒含有率: 54.61 % |
---|---|
結晶化 | 温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5 詳細: Calcium chloride, potassium chloride, sodium acetate |
-データ収集
回折 | 平均測定温度: 98.15 K / Serial crystal experiment: N |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2019年8月26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 Å / 相対比: 1 |
反射 | 解像度: 3→48.12 Å / Num. obs: 88754 / % possible obs: 98.6 % / 冗長度: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.056 / Rrim(I) all: 0.079 / Net I/σ(I): 12 |
反射 シェル | 解像度: 3→3.05 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1 / Num. unique obs: 4306 / CC1/2: 0.539 / Rpim(I) all: 0.883 / % possible all: 93.7 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: 3ut9 解像度: 3→48.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.432 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 327.1 Å2 / Biso mean: 118.078 Å2 / Biso min: 47.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 3→48.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|