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万見- EMDB-17008: CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17008 | |||||||||||||||
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タイトル | CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 | |||||||||||||||
マップデータ | ctINO80-hexasome focused cryoEM map Hexasome sharpened map | |||||||||||||||
試料 |
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キーワード | ATP-dependent chromatin remodeler / DNA BINDING PROTEIN | |||||||||||||||
機能・相同性 | 機能・相同性情報 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 / 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 ...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 / 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 / heterochromatin formation / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / 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 / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / 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 / identical protein binding / membrane / nucleus / cytosol 類似検索 - 分子機能 | |||||||||||||||
生物種 | Thermochaetoides thermophila (菌類) / synthetic construct (人工物) / Homo sapiens (ヒト) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.18 Å | |||||||||||||||
データ登録者 | Zhang M / Jungblut A / Hoffmann T / Eustermann S | |||||||||||||||
資金援助 | ドイツ, European Union, 4件
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引用 | ジャーナル: Acta Crystallogr D Biol Crystallogr / 年: 2010 タイトル: Features and development of Coot. 著者: P Emsley / B Lohkamp / W G Scott / K Cowtan / 要旨: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed. | |||||||||||||||
履歴 |
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-構造の表示
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 | emd_17008.map.gz | 5.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17008-v30.xml emd-17008.xml | 30.5 KB 30.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17008_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_17008.png | 166.8 KB | ||
Filedesc metadata | emd-17008.cif.gz | 8 KB | ||
その他 | emd_17008_additional_1.map.gz emd_17008_half_map_1.map.gz emd_17008_half_map_2.map.gz | 140.6 MB 140.9 MB 140.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17008 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17008 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_17008_validation.pdf.gz | 803.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_17008_full_validation.pdf.gz | 802.9 KB | 表示 | |
XML形式データ | emd_17008_validation.xml.gz | 20.4 KB | 表示 | |
CIF形式データ | emd_17008_validation.cif.gz | 27 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17008 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17008 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ooaMC 8oo7C 8oo9C 8oocC 8oofC 8ookC 8oopC 8oorC 8oosC 8ootC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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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
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_17008.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | ctINO80-hexasome focused cryoEM map Hexasome sharpened map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.822 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: ctINO80-hexasome focused cryoEM map Hexasome unsharpened map
ファイル | emd_17008_additional_1.map | ||||||||||||
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注釈 | ctINO80-hexasome focused cryoEM map Hexasome unsharpened map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: ctINO80-hexasome focused cryoEM map Hexasome half map
ファイル | emd_17008_half_map_1.map | ||||||||||||
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注釈 | ctINO80-hexasome focused cryoEM map Hexasome half map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: ctINO80-hexasome focused cryoEM map Hexasome half map
ファイル | emd_17008_half_map_2.map | ||||||||||||
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注釈 | ctINO80-hexasome focused cryoEM map Hexasome half map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : INO80 core module in complex with hexasome
全体 | 名称: INO80 core module in complex with hexasome |
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要素 |
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-超分子 #1: INO80 core module in complex with hexasome
超分子 | 名称: INO80 core module in complex with hexasome / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct ...詳細: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct INO80 + hexasome has an overall weight of 1.1MDa Ino80, Ies2, Ies6, Ies4,Arp6, Rvb1, Rvb2, Arp8, Arp4, Actin, Taf14 Hexasome DNA, 2xH3, 2xH4, H2A, H2B |
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由来(天然) | 生物種: Thermochaetoides thermophila (菌類) |
分子量 | 理論値: 861 KDa |
-分子 #1: DNA strand 1
分子 | 名称: DNA strand 1 / タイプ: dna / ID: 1 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: synthetic construct (人工物) |
分子量 | 理論値: 69.527195 KDa |
配列 | 文字列: (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) (DC)(DA)(DA)(DG)(DC) ...文字列: (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) (DC)(DA)(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)(DT)(DT)(DG)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DA)(DG) (DT) (DC)(DG)(DG)(DA)(DT)(DA)(DG)(DT)(DG)(DT) (DT)(DC)(DC)(DG)(DA)(DG)(DC)(DT)(DC) (DC)(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DG)(DG)(DA)(DT)(DC)(DC)(DC)(DC)(DG)(DG) (DG)(DT)(DA)(DC)(DC)(DG) |
-分子 #2: DNA Strand 2
分子 | 名称: DNA Strand 2 / タイプ: dna / ID: 2 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: synthetic construct (人工物) |
分子量 | 理論値: 70.043562 KDa |
配列 | 文字列: (DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT) (DA)(DT)(DC)(DC)(DG) ...文字列: (DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT) (DA)(DT)(DC)(DC)(DG)(DA)(DC)(DT) (DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA) (DA)(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)(DT)(DG)(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) |
-分子 #3: Histone H3.1
分子 | 名称: Histone H3.1 / 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: Homo sapiens (ヒト) |
分子量 | 理論値: 15.305969 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: Histone H3.1 |
-分子 #4: Histone H4
分子 | 名称: Histone H4 / 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: Homo sapiens (ヒト) |
分子量 | 理論値: 11.263231 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG UniProtKB: Histone H4 |
-分子 #5: Histone H2A
分子 | 名称: Histone H2A / タイプ: protein_or_peptide / ID: 5 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 14.004329 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: SGRGKQGGKA RAKAKSRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK UniProtKB: Histone H2A type 1-C |
-分子 #6: Histone H2B
分子 | 名称: Histone H2B / タイプ: protein_or_peptide / ID: 6 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 13.806018 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK UniProtKB: Histone H2B type 1-C/E/F/G/I |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.88 mg/mL |
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緩衝液 | pH: 7.5 詳細: 30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside |
グリッド | モデル: Quantifoil R2/1 / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 時間: 15 sec. / 詳細: 10% Oxygene 90% Argone |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 281 K / 装置: FEI VITROBOT MARK IV 詳細: wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807). |
詳細 | 11-subunit ctINO80 reconstituted with hexasome |
-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 K3 (6k x 4k) / 実像数: 15384 / 平均電子線量: 50.36 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |