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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-22684 | |||||||||
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タイトル | Cryo-EM structure of a chromatosome containing human linker histone H1.4 | |||||||||
![]() | sharpened map of H1.4 chromatosome for structure model building | |||||||||
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![]() | chromatosome / nucleosome / linker histones / Single-chain antibody / charge-charge interaction / chromatin / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | |||||||||
機能・相同性 | ![]() negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity ...negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / heterochromatin / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / euchromatin / heterochromatin formation / chromatin DNA binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / double-stranded DNA binding / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.76 Å | |||||||||
![]() | Zhou B-R / Bai Y | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. 著者: Bing-Rui Zhou / Hanqiao Feng / Seyit Kale / Tara Fox / Htet Khant / Natalia de Val / Rodolfo Ghirlando / Anna R Panchenko / Yawen Bai / ![]() ![]() ![]() 要旨: The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they ...The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 118.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 18.4 KB 18.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 116.7 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 508.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 508.5 KB | 表示 | |
XML形式データ | ![]() | 6.8 KB | 表示 | |
CIF形式データ | ![]() | 7.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7k5yMC ![]() 7k5xC ![]() 7k60C ![]() 7k61C ![]() 7k63C M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 208.9 Data #1: Unaligned multi-frames micrograph of a chomatosome containing human linker histone H1.4 [micrographs - multiframe]) |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | sharpened map of H1.4 chromatosome for structure model building | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.008 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : chromatosome containing human linker histone H1.4
全体 | 名称: chromatosome containing human linker histone H1.4 |
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要素 |
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-超分子 #1: chromatosome containing human linker histone H1.4
超分子 | 名称: chromatosome containing human linker histone H1.4 / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#8 |
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由来(天然) | 生物種: ![]() |
-分子 #1: Histone H3.1
分子 | 名称: Histone H3.1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 15.437167 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.1 |
-分子 #2: Histone H4
分子 | 名称: Histone H4 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 11.394426 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Arachidonate 15-lipoxygenase |
-分子 #3: Histone H2A type 1-B/E
分子 | 名称: Histone H2A type 1-B/E / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 14.165551 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K UniProtKB: Histone H2A type 1-B/E |
-分子 #4: Histone H2B type 1-J
分子 | 名称: Histone H2B type 1-J / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 13.935239 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK UniProtKB: Histone H2B type 1-J |
-分子 #7: scFv20
分子 | 名称: scFv20 / タイプ: protein_or_peptide / ID: 7 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 29.34542 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV ...文字列: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV KMPCKASGYT FTSYTIQWVK QTPRQGLEWI GYIYPYNAGT KYNEKFKGKA TLTSDKSSST VYMELSSLTS ED SAVYYCA RKSSRLRSTL DYWGQGTSVT VSS |
-分子 #8: Histone H1.4
分子 | 名称: Histone H1.4 / タイプ: protein_or_peptide / ID: 8 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 21.931521 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MSETAPAAPA APAPAEKTPV KKKARKSAGA AKRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK AKKAGAAKAK KPAGAAKKPK KATGAATPKK SAKKTPKKAK K PAAAAGAK ...文字列: MSETAPAAPA APAPAEKTPV KKKARKSAGA AKRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK AKKAGAAKAK KPAGAAKKPK KATGAATPKK SAKKTPKKAK K PAAAAGAK KAKSPKKAKA AKPKKAPKSP AKAKAVKPKA AKPKTAKPKA AKPKKAAAKK K UniProtKB: Histone H1.4 |
-分子 #5: DNA (197-MER)
分子 | 名称: DNA (197-MER) / タイプ: dna / ID: 5 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 60.510484 KDa |
配列 | 文字列: (DG)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DC) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT) (DG)(DC)(DC)(DG)(DA) ...文字列: (DG)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DC) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT) (DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT) (DC)(DG)(DT)(DA)(DG)(DA)(DC) (DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA) (DC)(DC)(DG) (DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT) (DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG) (DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC) (DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC) (DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG) (DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA) (DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT) (DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT) (DT) (DG)(DA)(DA)(DC)(DA)(DG)(DC)(DG)(DA)(DC) (DC)(DA)(DC)(DC)(DC)(DC) |
-分子 #6: DNA (197-MER)
分子 | 名称: DNA (197-MER) / タイプ: dna / ID: 6 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 61.141883 KDa |
配列 | 文字列: (DG)(DG)(DG)(DG)(DT)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG) (DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DC)(DT)(DG)(DA)(DC) ...文字列: (DG)(DG)(DG)(DG)(DT)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG) (DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT) (DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG) (DG)(DT)(DT)(DA)(DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA) (DC)(DA)(DG)(DC) (DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT) (DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT) (DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT) (DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG) (DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC) (DG)(DT)(DA)(DT)(DA)(DG)(DG)(DG)(DT)(DC) (DC)(DA)(DG)(DC)(DC)(DC) |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: OTHER / 撮影モード: OTHER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: 詳細: input pdb models: 4QLC, 6DZT, 5NL0 5Y0C |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.76 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC (ver. 2) / 使用した粒子像数: 112385 |
初期 角度割当 | タイプ: NOT APPLICABLE |
最終 角度割当 | タイプ: NOT APPLICABLE |