+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 3w97 | ||||||
---|---|---|---|---|---|---|---|
タイトル | Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region | ||||||
![]() |
| ||||||
![]() | STRUCTURAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / HISTONE-FOLD / NUCLEOSOME / STRUCTURAL PROTEIN-DNA complex | ||||||
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 / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine ...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 / heterochromatin organization / epigenetic regulation of gene expression / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / antibacterial humoral response / 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 / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Iwasaki, W. / Miya, Y. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Shibata, T. / Kagawa, W. / Kurumizaka, H. | ||||||
![]() | ![]() タイトル: Contribution of histone N-terminal tails to the structure and stability of nucleosomes 著者: Iwasaki, W. / Miya, Y. / Horikoshi, N. / Osakabe, A. / Taguchi, H. / Tachiwana, H. / Shibata, T. / Kagawa, W. / Kurumizaka, H. | ||||||
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 | ![]() | 320.3 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 243.1 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 | ![]() | 510.6 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 592.7 KB | 表示 | |
XML形式データ | ![]() | 44.9 KB | 表示 | |
CIF形式データ | ![]() | 62.5 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 |
| ||||||||
単位格子 |
|
-
要素
-タンパク質 , 4種, 8分子 AEBFCGDH
#1: タンパク質 | 分子量: 15719.445 Da / 分子数: 2 / 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 プラスミド: pHCE / 発現宿主: ![]() ![]() #2: タンパク質 | 分子量: 11676.703 Da / 分子数: 2 / 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 プラスミド: pET15b / 発現宿主: ![]() ![]() #3: タンパク質 | 分子量: 14447.825 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #4: タンパク質 | 分子量: 11751.545 Da / 分子数: 2 / Fragment: UNP residues 26-126 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
---|
-DNA鎖 / 非ポリマー , 2種, 3分子 IJ![](data/chem/img/MN.gif)
![](data/chem/img/MN.gif)
#5: DNA鎖 | 分子量: 45053.855 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: Palindromic 146-bp human alpha-satellite repeat #6: 化合物 | ChemComp-MN / | |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.58 Å3/Da / 溶媒含有率: 52.35 % |
---|---|
結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6 詳細: POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2010年10月7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: 3.2→50 Å / Num. obs: 33745 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 7.2 % / Rsym value: 0.095 |
反射 シェル | 解像度: 3.2→3.26 Å / 冗長度: 4.9 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 867 / Rsym value: 0.561 / % possible all: 50.9 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 3AFA 解像度: 3.2→48.71 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3099553.85 / Data cutoff low absF: 0 / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
| ||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 44.1749 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.2→48.71 Å
| ||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||
LS精密化 シェル | 解像度: 3.2→3.31 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||
Xplor file |
|