+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17027 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 | |||||||||||||||
マップデータ | ctINO80 hexasome complex focused cryoEM map ATPase hexasome sharpened map | |||||||||||||||
試料 |
| |||||||||||||||
キーワード | ATP-dependent chromatin remodeler / DNA BINDING PROTEIN (DNA結合タンパク質) | |||||||||||||||
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 / 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メチル化 / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / 遺伝的組換え / 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 / UCH proteinases / ヌクレオソーム / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / 遺伝子発現 / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / antibacterial humoral response / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / 核質 / 生体膜 / identical protein binding / 細胞核 / 細胞質基質 類似検索 - 分子機能 | |||||||||||||||
生物種 | Thermochaetoides thermophila (菌類) / Homo sapiens (ヒト) / Synthetic construct (人工物) / synthetic construct (人工物) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.29 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
| |||||||||||||||
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 |
|
-構造の表示
添付画像 |
---|
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_17027.map.gz | 5.6 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-17027-v30.xml emd-17027.xml | 38 KB 38 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17027_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_17027.png | 148 KB | ||
その他 | emd_17027_additional_1.map.gz emd_17027_half_map_1.map.gz emd_17027_half_map_2.map.gz | 140.6 MB 141.1 MB 141.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17027 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17027 | HTTPS FTP |
-関連構造データ
関連構造データ | 8oosMC 8oo7C 8oo9C 8ooaC 8oocC 8oofC 8ookC 8oopC 8oorC 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 |
---|---|
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 |
---|---|
「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_17027.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | ctINO80 hexasome complex focused cryoEM map ATPase hexasome sharpened map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.822 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-追加マップ: ctINO80 hexasome complex focused cryoEM map ATPase hexasome...
ファイル | emd_17027_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | ctINO80 hexasome complex focused cryoEM map ATPase hexasome unsharpened map | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: ctINO80 hexasome complex focused cryoEM map ATPase hexasome half map
ファイル | emd_17027_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | ctINO80 hexasome complex focused cryoEM map ATPase hexasome half map | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: ctINO80 hexasome complex focused cryoEM map ATPase hexasome half map
ファイル | emd_17027_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | ctINO80 hexasome complex focused cryoEM map ATPase hexasome half map | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : INO80 core module in complex with hexasome
+超分子 #1: INO80 core module in complex with hexasome
+超分子 #2: INO80
+超分子 #3: Histones
+超分子 #4: DNA
+分子 #1: Chromatin-remodeling ATPase Ino80
+分子 #4: Histone H3.1
+分子 #5: Histone H4
+分子 #6: Histone H2A
+分子 #7: Histone H2B
+分子 #2: DNA strand 1
+分子 #3: DNA Strand 2
+分子 #8: ADENOSINE-5'-DIPHOSPHATE
+分子 #9: MAGNESIUM ION
+分子 #10: TETRAFLUOROALUMINATE ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
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 / 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: Oxygen 10% Argon 90% |
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 |
---|---|
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 FIELDBright-field microscopy / 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 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
-原子モデル構築 1
初期モデル |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
精密化 | プロトコル: OTHER | ||||||||
得られたモデル | PDB-8oos: |