+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7xvl | |||||||||
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タイトル | Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) | |||||||||
要素 |
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キーワード | DNA BINDING PROTEIN/DNA / linker histone / nucleosome binding / chromatin structure / chromatin compaction / histone variants / STRUCTURAL PROTEIN-DNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of DNA recombination / positive regulation of transcription regulatory region DNA binding / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes ...negative regulation of DNA recombination / positive regulation of transcription regulatory region DNA binding / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / 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 formation / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / nucleosome binding / 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 / transcription repressor complex / 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 / euchromatin / 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 / chromatin DNA binding / 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 / actin cytoskeleton / 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 / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / chromatin / Golgi apparatus / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) synthetic construct (人工物) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.506 Å | |||||||||
データ登録者 | Adhireksan, Z. / Qiuye, B. / Lee, P.L. / Sharma, D. / Padavattan, S. / Davey, C.A. | |||||||||
資金援助 | シンガポール, 2件
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引用 | ジャーナル: To Be Published タイトル: Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) 著者: Adhireksan, Z. / Sharma, D. / Qiuye, B. / Lee, P.L. / Padavattan, S. / Davey, C.A. | |||||||||
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 | 7xvl.cif.gz | 1.3 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7xvl.ent.gz | 1 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7xvl.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 | 7xvl_validation.pdf.gz | 670.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7xvl_full_validation.pdf.gz | 697.3 KB | 表示 | |
XML形式データ | 7xvl_validation.xml.gz | 124.1 KB | 表示 | |
CIF形式データ | 7xvl_validation.cif.gz | 181.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/xv/7xvl ftp://data.pdbj.org/pub/pdb/validation_reports/xv/7xvl | HTTPS FTP |
-関連構造データ
関連構造データ | 3ut9S 4qlcS S: 精密化の開始モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
-タンパク質 , 5種, 33分子 AEKOUYeiBFLPVZfjCGMQWagkDHNRXb...
#1: タンパク質 | 分子量: 15581.299 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P68431 #2: タンパク質 | 分子量: 11538.556 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62805 #3: タンパク質 | 分子量: 14309.679 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P04908 #4: タンパク質 | 分子量: 14079.370 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: H2BC11, H2BFR, HIST1H2BJ / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P06899 #7: タンパク質 | | 分子量: 20950.152 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: H1-0, H1F0, H1FV / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P07305 |
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-DNA鎖 , 2種, 8分子 IScmJTdn
#5: DNA鎖 | 分子量: 52008.266 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌) #6: DNA鎖 | 分子量: 52330.262 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌) |
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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: 2.66 Å3/Da / 溶媒含有率: 53.85 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5) |
-データ収集
回折 | 平均測定温度: 98.15 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: SLS / ビームライン: X06DA / 波長: 1 Å |
検出器 | タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2017年9月17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: 3.506→88.439 Å / Num. obs: 117231 / % possible obs: 100 % / 冗長度: 6.1 % / CC1/2: 1 / Net I/σ(I): 8 |
反射 シェル | 解像度: 3.51→3.57 Å / 冗長度: 5.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5763 / CC1/2: 0.37 / % 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: 分子置換 開始モデル: 3UT9, 4QLC 解像度: 3.506→88.439 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.2 / SU B: 43.628 / SU ML: 0.639 / Average fsc free: 0.8426 / Average fsc work: 0.8744 / 交差検証法: THROUGHOUT / ESU R Free: 0.691 / 詳細: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 147.315 Å2
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精密化ステップ | サイクル: LAST / 解像度: 3.506→88.439 Å
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拘束条件 |
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LS精密化 シェル |
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