+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6jr1 | |||||||||||||||||||||
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タイトル | Crystal structure of the human nucleosome phased with 16 selenium atoms | |||||||||||||||||||||
要素 |
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キーワード | GENE REGULATION/DNA / nucleosome / chromatin / histone / selenomethionine / SAD phasing / GENE REGULATION / GENE REGULATION-DNA complex | |||||||||||||||||||||
機能・相同性 | 機能・相同性情報 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 / 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 / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / 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 / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Meiotic recombination / Metalloprotease DUBs / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / antibacterial humoral response / 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 / Processing of DNA double-strand break ends / gene expression / 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 | Homo sapiens (ヒト) | |||||||||||||||||||||
手法 | X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.4 Å | |||||||||||||||||||||
データ登録者 | Saotome, M. / Horikoshi, N. / Urano, K. / Kujirai, T. / Yuzurihara, H. / Kurumizaka, H. / Kagawa, W. | |||||||||||||||||||||
資金援助 | 日本, 6件
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引用 | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019 タイトル: Structure determination of the nucleosome core particle by selenium SAD phasing. 著者: Saotome, M. / Horikoshi, N. / Urano, K. / Kujirai, T. / Yuzurihara, H. / Kurumizaka, H. / Kagawa, W. | |||||||||||||||||||||
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 | 6jr1.cif.gz | 340.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6jr1.ent.gz | 258.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6jr1.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
文書・要旨 | 6jr1_validation.pdf.gz | 517.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6jr1_full_validation.pdf.gz | 531.6 KB | 表示 | |
XML形式データ | 6jr1_validation.xml.gz | 48.4 KB | 表示 | |
CIF形式データ | 6jr1_validation.cif.gz | 67.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jr/6jr1 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/6jr1 | HTTPS FTP |
-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
-タンパク質 , 4種, 8分子 AEBFCGDH
#1: タンパク質 | 分子量: 15860.131 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 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: pET15b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834(DE3) / 参照: UniProt: P68431 #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) Homo sapiens (ヒト) 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: Escherichia coli (大腸菌) / 株 (発現宿主): JM109(DE3) / 参照: UniProt: P62805 #3: タンパク質 | 分子量: 14624.589 Da / 分子数: 2 / Mutation: L65M, L85M / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / プラスミド: pET15b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834(DE3) / 参照: UniProt: P04908 #4: タンパク質 | 分子量: 14488.070 Da / 分子数: 2 / Mutation: L101M, L106M / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HIST1H2BJ, H2BFR / プラスミド: pHCE / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834(DE3) / 参照: UniProt: P06899 |
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-DNA鎖 , 1種, 2分子 IJ
#5: DNA鎖 | 分子量: 45053.855 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) |
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-非ポリマー , 3種, 577分子
#6: 化合物 | ChemComp-CL / #7: 化合物 | ChemComp-MN / #8: 水 | ChemComp-HOH / | |
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-詳細
Has protein modification | Y |
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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: 2.26 Å3/Da / 溶媒含有率: 45.62 % |
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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 |
-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: Photon Factory / ビームライン: BL-1A / 波長: 0.9793 Å |
検出器 | タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2016年3月21日 |
放射 | モノクロメーター: Cryo-cooled channel-cut Si(111) / 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: 0.9793 Å / 相対比: 1 |
反射 | 解像度: 2.4→47.74 Å / Num. obs: 72878 / % possible obs: 100 % / 冗長度: 14 % / Biso Wilson estimate: 25.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.049 / Rrim(I) all: 0.138 / Net I/σ(I): 15.7 |
反射 シェル | 解像度: 2.4→2.45 Å / 冗長度: 13.3 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4431 / CC1/2: 0.845 / Rpim(I) all: 0.387 / Rrim(I) all: 1.029 / % possible all: 100 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.4→47.74 Å / SU ML: 0.31 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 26.01
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.4→47.74 Å
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拘束条件 |
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LS精密化 シェル |
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