+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30239 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C | ||||||||||||
マップデータ | |||||||||||||
試料 |
| ||||||||||||
機能・相同性 | 機能・相同性情報 Interleukin-7 signaling / Chromatin modifying enzymes / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...Interleukin-7 signaling / Chromatin modifying enzymes / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / Factors involved in megakaryocyte development and platelet production / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / detection of maltose stimulus / maltose transport complex / carbohydrate transport / establishment of mitotic spindle orientation / carbohydrate transmembrane transporter activity / maltose binding / mitotic cytokinesis / maltose transport / negative regulation of tumor necrosis factor-mediated signaling pathway / maltodextrin transmembrane transport / negative regulation of megakaryocyte differentiation / heterochromatin organization / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / RNA Polymerase I Promoter Opening / ATP-binding cassette (ABC) transporter complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / cell chemotaxis / 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 / lipopolysaccharide binding / 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 / kinetochore / 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 / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / outer membrane-bounded periplasmic space / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium 類似検索 - 分子機能 | ||||||||||||
生物種 | Gallus gallus (ニワトリ) / Homo sapiens (ヒト) / 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: 4.5 Å | ||||||||||||
データ登録者 | Ariyoshi M / Makino F / Fukagawa T | ||||||||||||
資金援助 | 日本, 3件
| ||||||||||||
引用 | ジャーナル: EMBO J / 年: 2021 タイトル: Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C. 著者: Mariko Ariyoshi / Fumiaki Makino / Reito Watanabe / Reiko Nakagawa / Takayuki Kato / Keiichi Namba / Yasuhiro Arimura / Risa Fujita / Hitoshi Kurumizaka / Ei-Ichi Okumura / Masatoshi Hara / Tatsuo Fukagawa / 要旨: The CENP-A nucleosome is a key structure for kinetochore assembly. Once the CENP-A nucleosome is established in the centromere, additional proteins recognize the CENP-A nucleosome to form a ...The CENP-A nucleosome is a key structure for kinetochore assembly. Once the CENP-A nucleosome is established in the centromere, additional proteins recognize the CENP-A nucleosome to form a kinetochore. CENP-C and CENP-N are CENP-A binding proteins. We previously demonstrated that vertebrate CENP-C binding to the CENP-A nucleosome is regulated by CDK1-mediated CENP-C phosphorylation. However, it is still unknown how the phosphorylation of CENP-C regulates its binding to CENP-A. It is also not completely understood how and whether CENP-C and CENP-N act together on the CENP-A nucleosome. Here, using cryo-electron microscopy (cryo-EM) in combination with biochemical approaches, we reveal a stable CENP-A nucleosome-binding mode of CENP-C through unique regions. The chicken CENP-C structure bound to the CENP-A nucleosome is stabilized by an intramolecular link through the phosphorylated CENP-C residue. The stable CENP-A-CENP-C complex excludes CENP-N from the CENP-A nucleosome. These findings provide mechanistic insights into the dynamic kinetochore assembly regulated by CDK1-mediated CENP-C phosphorylation. | ||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
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_30239.map.gz | 34 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-30239-v30.xml emd-30239.xml | 26.7 KB 26.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_30239_fsc.xml | 7.6 KB | 表示 | FSCデータファイル |
画像 | emd_30239.png | 32.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30239 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30239 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30239_validation.pdf.gz | 462.4 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_30239_full_validation.pdf.gz | 462 KB | 表示 | |
XML形式データ | emd_30239_validation.xml.gz | 9.8 KB | 表示 | |
CIF形式データ | emd_30239_validation.cif.gz | 12.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30239 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30239 | HTTPS FTP |
-関連構造データ
関連構造データ | 7by0MC 7bxtC 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 (文献) |
---|---|
類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10565 (タイトル: The cryo-EM structure of the CENP-A nucleosome in complex with the phosphorylated CENP-C: CENP-A nucleosome in complex with phosphorylated CENP-C C-terminal domain (601-864) and CENP-N ...タイトル: The cryo-EM structure of the CENP-A nucleosome in complex with the phosphorylated CENP-C: CENP-A nucleosome in complex with phosphorylated CENP-C C-terminal domain (601-864) and CENP-N N-terminal domain (1-211) Data size: 1.6 TB Data #1: CENP-A nucleosome in complex with phosphorylated CENP-C C-terminal domain (601-864) and CENP-N N-terminal domain (1-211) [micrographs - multiframe]) |
-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_30239.map.gz / 形式: CCP4 / 大きさ: 36.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
+全体 : CENP-A nucleosome in complex with CENP-C C-terminal and CNEP-N N-...
+超分子 #1: CENP-A nucleosome in complex with CENP-C C-terminal and CNEP-N N-...
+超分子 #2: Histone H3,Histone H3-like centromeric protein A
+超分子 #3: Histone H4
+超分子 #4: Histone H2A type 1-B/E
+超分子 #5: Histone H2B type 1-J
+超分子 #6: DNA (145-mer)
+超分子 #7: Maltodextrin-binding protein,LINKER PEPTIDE,CENP-C
+分子 #1: Histone H3.2,Histone H3-like centromeric protein A
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-B/E
+分子 #4: Histone H2B type 1-J
+分子 #7: Maltose Binding Protein tag, linker,CENP-C
+分子 #5: DNA (145-MER)
+分子 #6: DNA (145-MER)
-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 | 0.5 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
緩衝液 | pH: 7.5 構成要素:
| ||||||||||||||||||
グリッド | モデル: Quantifoil R0.6/1 / 材質: MOLYBDENUM / 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 ARRAY / 支持フィルム - Film thickness: 300.0 nm / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR | ||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | JEOL CRYO ARM 200 |
---|---|
温度 | 最低: 80.0 K / 最高: 80.0 K |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / デジタル化 - サイズ - 横: 3838 pixel / デジタル化 - サイズ - 縦: 3710 pixel / デジタル化 - サンプリング間隔: 5.0 µm / デジタル化 - 画像ごとのフレーム数: 1-50 / 撮影したグリッド数: 5 / 実像数: 5346 / 平均露光時間: 10.0 sec. / 平均電子線量: 1.2 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 150.0 µm / 最大 デフォーカス(補正後): -7.0 µm / 最小 デフォーカス(補正後): -0.5 µm / 倍率(補正後): 45454 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 1.4 mm / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 50000 |
試料ステージ | 試料ホルダーモデル: JEOL CRYOSPECPORTER / ホルダー冷却材: NITROGEN |