+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17226 | |||||||||||||||
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タイトル | Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
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キーワード | kinetochore / point centromere / CENP-A nucleosome / topological entrapment / centromeric DNA / CELL CYCLE | |||||||||||||||
機能・相同性 | 機能・相同性情報 Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / HDMs demethylate histones / PKMTs methylate histone lysines ...Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / HDMs demethylate histones / PKMTs methylate histone lysines / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / attachment of spindle microtubules to kinetochore / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / centromeric DNA binding / Assembly of the ORC complex at the origin of replication / CENP-A containing chromatin assembly / HDACs deacetylate histones / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly / condensed chromosome, centromeric region / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / spindle pole body / protein localization to kinetochore / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / positive regulation of transcription by RNA polymerase I / mitotic spindle assembly checkpoint signaling / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / mitotic sister chromatid segregation / Estrogen-dependent gene expression / rRNA transcription / chromosome, centromeric region / DNA replication initiation / heterochromatin organization / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / nucleosomal DNA binding / meiotic cell cycle / chromosome segregation / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / protein dimerization activity / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / DNA repair / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus / cytoplasm 類似検索 - 分子機能 | |||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||||||||
データ登録者 | Dendooven TD / Zhang Z / Yang J / McLaughlin S / Schwabb J / Scheres S / Yatskevich S / Barford D | |||||||||||||||
資金援助 | 英国, ドイツ, 4件
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引用 | ジャーナル: Sci Adv / 年: 2023 タイトル: Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere. 著者: Tom Dendooven / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / Johannes Schwab / Sjors H W Scheres / Stanislau Yatskevich / David Barford / 要旨: The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) ...The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-A). This revealed a central CENP-A with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-A can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle. | |||||||||||||||
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_17226.map.gz | 165.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17226-v30.xml emd-17226.xml | 41.3 KB 41.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_17226.png | 63 KB | ||
Filedesc metadata | emd-17226.cif.gz | 10.4 KB | ||
その他 | emd_17226_additional_1.map.gz emd_17226_half_map_1.map.gz emd_17226_half_map_2.map.gz | 106.7 MB 165.5 MB 165.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17226 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17226 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_17226_validation.pdf.gz | 1.4 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_17226_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | emd_17226_validation.xml.gz | 8.7 KB | 表示 | |
CIF形式データ | emd_17226_validation.cif.gz | 7.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17226 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17226 | HTTPS FTP |
-関連構造データ
-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_17226.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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ボクセルのサイズ | X=Y=Z: 0.853 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: #1
ファイル | emd_17226_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_17226_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_17226_half_map_2.map | ||||||||||||
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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 : A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+超分子 #1: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+分子 #1: C0N3 DNA
+分子 #2: C0N3 DNA
+分子 #3: Histone H4
+分子 #4: Histone H2B.1
+分子 #5: Histone H3-like centromeric protein CSE4
+分子 #6: Histone H2A.1
+分子 #7: Centromere-binding protein 1
+分子 #8: Inner kinetochore subunit MCM16
+分子 #9: Inner kinetochore subunit CTF3
+分子 #10: Inner kinetochore subunit MCM22
+分子 #11: Inner kinetochore subunit IML3
+分子 #12: Inner kinetochore subunit CHL4
+分子 #13: Inner kinetochore subunit MCM21
+分子 #14: Inner kinetochore subunit CTF19
+分子 #15: Inner kinetochore subunit OKP1
+分子 #16: Inner kinetochore subunit CNN1
+分子 #17: Inner kinetochore subunit AME1
+分子 #18: Inner kinetochore subunit WIP1
+分子 #19: Inner kinetochore subunit NKP1
+分子 #20: Inner kinetochore subunit NKP2
-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
緩衝液 | pH: 8 |
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凍結 | 凍結剤: ETHANE |
-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 BIOQUANTUM (6k 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: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.6 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 100311 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |